<?xml version="1.0" encoding="UTF-8"?>

<!--XBRL Document Created with the Workiva Platform-->
<!--Copyright 2026 Workiva-->
<!--r:019e6c04-3b5f-725a-82ef-46cfd3592b7a,g:868a9f83-0b37-4e6f-afe9-a5f0e84e0d78-->
<link:linkbase xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/all" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#all"/>
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#hypercube-dimension"/>
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-default"/>
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-domain"/>
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/domain-member" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#domain-member"/>
  <link:roleRef roleURI="http://www.codexis.com/role/CondensedConsolidatedStatementsofOperations" xlink:type="simple" xlink:href="cdxs-20260630.xsd#CondensedConsolidatedStatementsofOperations"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/CondensedConsolidatedStatementsofOperations" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementTable_019e6c04-3c30-71a6-b9cc-d7cf2643604a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_StatementTable_019e6c04-3c30-71a6-b9cc-d7cf2643604a" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_ProductOrServiceAxis_019e6c04-3c30-71cd-8660-6f5903e42716" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductOrServiceAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_StatementTable_019e6c04-3c30-71a6-b9cc-d7cf2643604a" xlink:to="loc_srt_ProductOrServiceAxis_019e6c04-3c30-71cd-8660-6f5903e42716" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_019e6c04-3c30-71cd-8660-6f5903e42716_default" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductsAndServicesDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_ProductOrServiceAxis_019e6c04-3c30-71cd-8660-6f5903e42716" xlink:to="loc_srt_ProductsAndServicesDomain_019e6c04-3c30-71cd-8660-6f5903e42716_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_ProductsAndServicesDomain_019e6c04-3c30-7010-8b45-3dbcb1db299c" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_ProductsAndServicesDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_ProductOrServiceAxis_019e6c04-3c30-71cd-8660-6f5903e42716" xlink:to="loc_srt_ProductsAndServicesDomain_019e6c04-3c30-7010-8b45-3dbcb1db299c" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProductMember_019e6c04-3c30-7936-b0a7-dca6f47469cc" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ProductMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_019e6c04-3c30-7010-8b45-3dbcb1db299c" xlink:to="loc_us-gaap_ProductMember_019e6c04-3c30-7936-b0a7-dca6f47469cc" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_ResearchandDevelopmentRevenueMember_019e6c04-3c30-76e9-8e8a-95247a63535a" xlink:href="cdxs-20260630.xsd#cdxs_ResearchandDevelopmentRevenueMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_ProductsAndServicesDomain_019e6c04-3c30-7010-8b45-3dbcb1db299c" xlink:to="loc_cdxs_ResearchandDevelopmentRevenueMember_019e6c04-3c30-76e9-8e8a-95247a63535a" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenuesAbstract_019e6c04-3c30-750f-a37f-69c26004e31d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenuesAbstract"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_RevenuesAbstract_019e6c04-3c30-750f-a37f-69c26004e31d" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_019e6c04-3c30-78dc-9175-f603dfece106" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_RevenuesAbstract_019e6c04-3c30-750f-a37f-69c26004e31d" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_019e6c04-3c30-78dc-9175-f603dfece106" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingCostsAndExpensesAbstract_019e6c04-3c30-71c0-84f9-9d9462863bf2" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingCostsAndExpensesAbstract"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_OperatingCostsAndExpensesAbstract_019e6c04-3c30-71c0-84f9-9d9462863bf2" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CostOfGoodsAndServicesSold_019e6c04-3c30-7581-839b-9d76874317c0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CostOfGoodsAndServicesSold"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OperatingCostsAndExpensesAbstract_019e6c04-3c30-71c0-84f9-9d9462863bf2" xlink:to="loc_us-gaap_CostOfGoodsAndServicesSold_019e6c04-3c30-7581-839b-9d76874317c0" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentExpense_019e6c04-3c30-7b9c-9a17-43c707a98128" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ResearchAndDevelopmentExpense"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OperatingCostsAndExpensesAbstract_019e6c04-3c30-71c0-84f9-9d9462863bf2" xlink:to="loc_us-gaap_ResearchAndDevelopmentExpense_019e6c04-3c30-7b9c-9a17-43c707a98128" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SellingGeneralAndAdministrativeExpense_019e6c04-3c30-7a91-8bd2-12688e09c56c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SellingGeneralAndAdministrativeExpense"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OperatingCostsAndExpensesAbstract_019e6c04-3c30-71c0-84f9-9d9462863bf2" xlink:to="loc_us-gaap_SellingGeneralAndAdministrativeExpense_019e6c04-3c30-7a91-8bd2-12688e09c56c" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CostsAndExpenses_019e6c04-3c30-7c0b-a86f-513ec981afa5" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CostsAndExpenses"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OperatingCostsAndExpensesAbstract_019e6c04-3c30-71c0-84f9-9d9462863bf2" xlink:to="loc_us-gaap_CostsAndExpenses_019e6c04-3c30-7c0b-a86f-513ec981afa5" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingIncomeLoss_019e6c04-3c30-73ab-948c-632a4d3a1474" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingIncomeLoss"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_OperatingIncomeLoss_019e6c04-3c30-73ab-948c-632a4d3a1474" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_InvestmentIncomeInterest_019e6c04-3c30-7d90-8055-800b142fd598" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InvestmentIncomeInterest"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_InvestmentIncomeInterest_019e6c04-3c30-7d90-8055-800b142fd598" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherNonoperatingIncomeExpense_019e6c04-3c30-7d03-83ef-52030a2def62" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherNonoperatingIncomeExpense"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_OtherNonoperatingIncomeExpense_019e6c04-3c30-7d03-83ef-52030a2def62" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest_019e6c04-3c30-7c05-ba03-7bd6b121113a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest_019e6c04-3c30-7c05-ba03-7bd6b121113a" xlink:type="arc" order="5"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncomeTaxExpenseBenefit_019e6c04-3c30-7c71-8787-314322974537" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncomeTaxExpenseBenefit"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_IncomeTaxExpenseBenefit_019e6c04-3c30-7c71-8787-314322974537" xlink:type="arc" order="6"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NetIncomeLoss_019e6c04-3c30-75f5-8433-22136c5cb65a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLoss"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_NetIncomeLoss_019e6c04-3c30-75f5-8433-22136c5cb65a" xlink:type="arc" order="7"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EarningsPerShareBasic_019e6c04-3c30-7279-b5c2-a7433a915d17" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareBasic"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_EarningsPerShareBasic_019e6c04-3c30-7279-b5c2-a7433a915d17" xlink:type="arc" order="8"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EarningsPerShareDiluted_019e6c04-3c30-7e4d-bd31-d8d22422599c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EarningsPerShareDiluted"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_EarningsPerShareDiluted_019e6c04-3c30-7e4d-bd31-d8d22422599c" xlink:type="arc" order="9"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_WeightedAverageNumberOfSharesOutstandingBasic_019e6c04-3c30-7e5b-a429-e0ed334f966c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_WeightedAverageNumberOfSharesOutstandingBasic"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_WeightedAverageNumberOfSharesOutstandingBasic_019e6c04-3c30-7e5b-a429-e0ed334f966c" xlink:type="arc" order="10"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding_019e6c04-3c30-7515-8b39-84e61f7b90a3" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7893-ad3e-38f9311f9c0d" xlink:to="loc_us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding_019e6c04-3c30-7515-8b39-84e61f7b90a3" xlink:type="arc" order="11"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/CondensedConsolidatedStatementsofStockholdersEquity" xlink:type="simple" xlink:href="cdxs-20260630.xsd#CondensedConsolidatedStatementsofStockholdersEquity"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/CondensedConsolidatedStatementsofStockholdersEquity" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementLineItems_019e6c04-3c30-7568-abee-0dcfb4540de6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementTable_019e6c04-3c30-708e-8ed1-884b6da731b5" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7568-abee-0dcfb4540de6" xlink:to="loc_us-gaap_StatementTable_019e6c04-3c30-708e-8ed1-884b6da731b5" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementEquityComponentsAxis_019e6c04-3c30-7293-9e05-70b58c5c2cab" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementEquityComponentsAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_StatementTable_019e6c04-3c30-708e-8ed1-884b6da731b5" xlink:to="loc_us-gaap_StatementEquityComponentsAxis_019e6c04-3c30-7293-9e05-70b58c5c2cab" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquityComponentDomain_019e6c04-3c30-7293-9e05-70b58c5c2cab_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EquityComponentDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_StatementEquityComponentsAxis_019e6c04-3c30-7293-9e05-70b58c5c2cab" xlink:to="loc_us-gaap_EquityComponentDomain_019e6c04-3c30-7293-9e05-70b58c5c2cab_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquityComponentDomain_019e6c04-3c30-7619-ae11-fedd70183510" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EquityComponentDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_StatementEquityComponentsAxis_019e6c04-3c30-7293-9e05-70b58c5c2cab" xlink:to="loc_us-gaap_EquityComponentDomain_019e6c04-3c30-7619-ae11-fedd70183510" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommonStockMember_019e6c04-3c30-7a02-8ba9-36cc73df5328" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommonStockMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquityComponentDomain_019e6c04-3c30-7619-ae11-fedd70183510" xlink:to="loc_us-gaap_CommonStockMember_019e6c04-3c30-7a02-8ba9-36cc73df5328" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AdditionalPaidInCapitalMember_019e6c04-3c30-729b-a69c-47871e7dd4f5" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AdditionalPaidInCapitalMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquityComponentDomain_019e6c04-3c30-7619-ae11-fedd70183510" xlink:to="loc_us-gaap_AdditionalPaidInCapitalMember_019e6c04-3c30-729b-a69c-47871e7dd4f5" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccumulatedOtherComprehensiveIncomeMember_019e6c04-3c30-7173-b9c5-87ec6dd2e3e3" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquityComponentDomain_019e6c04-3c30-7619-ae11-fedd70183510" xlink:to="loc_us-gaap_AccumulatedOtherComprehensiveIncomeMember_019e6c04-3c30-7173-b9c5-87ec6dd2e3e3" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_RetainedEarningsMember_019e6c04-3c30-7c83-ac68-f6dfbbdd5852" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RetainedEarningsMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EquityComponentDomain_019e6c04-3c30-7619-ae11-fedd70183510" xlink:to="loc_us-gaap_RetainedEarningsMember_019e6c04-3c30-7c83-ac68-f6dfbbdd5852" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInStockholdersEquityRollForward"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_StatementLineItems_019e6c04-3c30-7568-abee-0dcfb4540de6" xlink:to="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharesOutstanding_019e6c04-3c30-7d1a-aa51-947237599e7d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SharesOutstanding"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:to="loc_us-gaap_SharesOutstanding_019e6c04-3c30-7d1a-aa51-947237599e7d" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockholdersEquity_019e6c04-3c30-76ce-9cd0-aa7af7775302" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockholdersEquity"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:to="loc_us-gaap_StockholdersEquity_019e6c04-3c30-76ce-9cd0-aa7af7775302" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised_019e6c04-3c30-7756-b7fc-b7a2aee7f6f5" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:to="loc_us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised_019e6c04-3c30-7756-b7fc-b7a2aee7f6f5" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised_019e6c04-3c30-7da2-a0b8-9bdfab82cace" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:to="loc_us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised_019e6c04-3c30-7da2-a0b8-9bdfab82cace" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodSharesOther_019e6c04-3c30-798e-a99a-8e717176834d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodSharesOther"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:to="loc_us-gaap_StockIssuedDuringPeriodSharesOther_019e6c04-3c30-798e-a99a-8e717176834d" xlink:type="arc" order="5"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans_019e8361-68a8-74cc-b29e-0c7e965e4853" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:to="loc_us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans_019e8361-68a8-74cc-b29e-0c7e965e4853" xlink:type="arc" order="6"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodValueEmployeeStockPurchasePlan_019e8361-d5be-7b19-b8a1-a89174f7460b" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodValueEmployeeStockPurchasePlan"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:to="loc_us-gaap_StockIssuedDuringPeriodValueEmployeeStockPurchasePlan_019e8361-d5be-7b19-b8a1-a89174f7460b" xlink:type="arc" order="7"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodSharesNewIssues_019e8362-e499-7006-9fd5-afb8111d59f6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:to="loc_us-gaap_StockIssuedDuringPeriodSharesNewIssues_019e8362-e499-7006-9fd5-afb8111d59f6" xlink:type="arc" order="8"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodValueNewIssues_019e8363-d2df-7678-8f13-53bfa2e83334" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodValueNewIssues"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:to="loc_us-gaap_StockIssuedDuringPeriodValueNewIssues_019e8363-d2df-7678-8f13-53bfa2e83334" xlink:type="arc" order="9"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue_019e6c04-3c30-7ce4-8fd6-dfb5e4c4a554" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:to="loc_us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue_019e6c04-3c30-7ce4-8fd6-dfb5e4c4a554" xlink:type="arc" order="10"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NetIncomeLoss_019e6c04-3c30-7e77-bd20-409ce124a909" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLoss"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:to="loc_us-gaap_NetIncomeLoss_019e6c04-3c30-7e77-bd20-409ce124a909" xlink:type="arc" order="11"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherComprehensiveIncomeLossNetOfTax_019e6c04-3c30-723a-9004-b057d9f3940d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherComprehensiveIncomeLossNetOfTax"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_IncreaseDecreaseInStockholdersEquityRollForward_019e6c04-3c30-7720-8f60-79807f51e875" xlink:to="loc_us-gaap_OtherComprehensiveIncomeLossNetOfTax_019e6c04-3c30-723a-9004-b057d9f3940d" xlink:type="arc" order="12"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SharesOutstanding_019e6c04-3c30-7a39-84d7-296c57bda7f6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SharesOutstanding"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockholdersEquity_019e6c04-3c30-7347-ac8d-7c8b9c88ab40" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockholdersEquity"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/RevenueRecognitionDisaggregationofRevenueDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#RevenueRecognitionDisaggregationofRevenueDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/RevenueRecognitionDisaggregationofRevenueDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DisaggregationOfRevenueLineItems_019e6c04-3c30-718f-9650-c6c39c357c89" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisaggregationOfRevenueLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DisaggregationOfRevenueTable_019e6c04-3c30-7453-bc7e-36aff3c424eb" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisaggregationOfRevenueTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_019e6c04-3c30-718f-9650-c6c39c357c89" xlink:to="loc_us-gaap_DisaggregationOfRevenueTable_019e6c04-3c30-7453-bc7e-36aff3c424eb" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_StatementGeographicalAxis_019e6c04-3c30-78e5-a121-ec33ee57fb08" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_StatementGeographicalAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DisaggregationOfRevenueTable_019e6c04-3c30-7453-bc7e-36aff3c424eb" xlink:to="loc_srt_StatementGeographicalAxis_019e6c04-3c30-78e5-a121-ec33ee57fb08" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_SegmentGeographicalDomain_019e6c04-3c30-78e5-a121-ec33ee57fb08_default" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_SegmentGeographicalDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_StatementGeographicalAxis_019e6c04-3c30-78e5-a121-ec33ee57fb08" xlink:to="loc_srt_SegmentGeographicalDomain_019e6c04-3c30-78e5-a121-ec33ee57fb08_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_SegmentGeographicalDomain_019e6c04-3c30-72bb-b220-18dc8ebdb530" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_SegmentGeographicalDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_StatementGeographicalAxis_019e6c04-3c30-78e5-a121-ec33ee57fb08" xlink:to="loc_srt_SegmentGeographicalDomain_019e6c04-3c30-72bb-b220-18dc8ebdb530" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_APACMember_019e6c04-3c30-7cd9-bb79-afcc894fcee2" xlink:href="cdxs-20260630.xsd#cdxs_APACMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_019e6c04-3c30-72bb-b220-18dc8ebdb530" xlink:to="loc_cdxs_APACMember_019e6c04-3c30-7cd9-bb79-afcc894fcee2" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_AmericasMember_019e6c04-3c30-7be4-be01-5568ab43f5f3" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_AmericasMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_019e6c04-3c30-72bb-b220-18dc8ebdb530" xlink:to="loc_srt_AmericasMember_019e6c04-3c30-7be4-be01-5568ab43f5f3" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EMEAMember_019e6c04-3c30-74e9-83e8-a265e4b65a9f" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EMEAMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_SegmentGeographicalDomain_019e6c04-3c30-72bb-b220-18dc8ebdb530" xlink:to="loc_us-gaap_EMEAMember_019e6c04-3c30-74e9-83e8-a265e4b65a9f" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_019e6c04-3c30-78dc-a879-655b43dab3fa" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_019e6c04-3c30-718f-9650-c6c39c357c89" xlink:to="loc_us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax_019e6c04-3c30-78dc-a879-655b43dab3fa" xlink:type="arc" order="0"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/RevenueRecognitionNarrativeDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#RevenueRecognitionNarrativeDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/RevenueRecognitionNarrativeDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DisaggregationOfRevenueLineItems_019e6c04-3c30-7c11-bd4d-a2cd07e4dc49" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisaggregationOfRevenueLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DisaggregationOfRevenueTable_019e6c04-3c30-7468-a88d-10a3cfe2137a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DisaggregationOfRevenueTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_019e6c04-3c30-7c11-bd4d-a2cd07e4dc49" xlink:to="loc_us-gaap_DisaggregationOfRevenueTable_019e6c04-3c30-7468-a88d-10a3cfe2137a" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccountsNotesLoansAndFinancingReceivableByReceivableTypeAxis_019e6c04-3c30-79fc-a32c-1c470d7993d0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccountsNotesLoansAndFinancingReceivableByReceivableTypeAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DisaggregationOfRevenueTable_019e6c04-3c30-7468-a88d-10a3cfe2137a" xlink:to="loc_us-gaap_AccountsNotesLoansAndFinancingReceivableByReceivableTypeAxis_019e6c04-3c30-79fc-a32c-1c470d7993d0" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ReceivableTypeDomain_019e6c04-3c30-79fc-a32c-1c470d7993d0_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ReceivableTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_AccountsNotesLoansAndFinancingReceivableByReceivableTypeAxis_019e6c04-3c30-79fc-a32c-1c470d7993d0" xlink:to="loc_us-gaap_ReceivableTypeDomain_019e6c04-3c30-79fc-a32c-1c470d7993d0_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ReceivableTypeDomain_019e6c04-3c30-7f00-8810-c0764a63a14a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ReceivableTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_AccountsNotesLoansAndFinancingReceivableByReceivableTypeAxis_019e6c04-3c30-79fc-a32c-1c470d7993d0" xlink:to="loc_us-gaap_ReceivableTypeDomain_019e6c04-3c30-7f00-8810-c0764a63a14a" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_ShortTermUnbilledReceivablesMember_019e6c04-3c30-7b5e-8924-4e8d62a7a186" xlink:href="cdxs-20260630.xsd#cdxs_ShortTermUnbilledReceivablesMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ReceivableTypeDomain_019e6c04-3c30-7f00-8810-c0764a63a14a" xlink:to="loc_cdxs_ShortTermUnbilledReceivablesMember_019e6c04-3c30-7b5e-8924-4e8d62a7a186" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_LongTermUnbilledReceivablesMember_019e6c04-3c30-770a-8218-eb174300f6ad" xlink:href="cdxs-20260630.xsd#cdxs_LongTermUnbilledReceivablesMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ReceivableTypeDomain_019e6c04-3c30-7f00-8810-c0764a63a14a" xlink:to="loc_cdxs_LongTermUnbilledReceivablesMember_019e6c04-3c30-770a-8218-eb174300f6ad" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ContractWithCustomerAssetCreditLossExpense_019e6c04-3c30-7345-b4b2-7e157406de21" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ContractWithCustomerAssetCreditLossExpense"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_019e6c04-3c30-7c11-bd4d-a2cd07e4dc49" xlink:to="loc_us-gaap_ContractWithCustomerAssetCreditLossExpense_019e6c04-3c30-7345-b4b2-7e157406de21" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_UnbilledReceivablesNotBillableAtBalanceSheetDate_019e6c04-3c30-7111-8c4e-8591bcfa4c45" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_UnbilledReceivablesNotBillableAtBalanceSheetDate"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_019e6c04-3c30-7c11-bd4d-a2cd07e4dc49" xlink:to="loc_us-gaap_UnbilledReceivablesNotBillableAtBalanceSheetDate_019e6c04-3c30-7111-8c4e-8591bcfa4c45" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_RevenueRemainingPerformanceObligation_019e6c04-3c30-74c5-9204-5faa1cd3e7fd" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueRemainingPerformanceObligation"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DisaggregationOfRevenueLineItems_019e6c04-3c30-7c11-bd4d-a2cd07e4dc49" xlink:to="loc_us-gaap_RevenueRemainingPerformanceObligation_019e6c04-3c30-74c5-9204-5faa1cd3e7fd" xlink:type="arc" order="2"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/NetLossperShareDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#NetLossperShareDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/NetLossperShareDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems_019e6c04-3c30-7597-a8fa-67d2749a9eab" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable_019e6c04-3c30-70ca-b756-bf2065a22304" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems_019e6c04-3c30-7597-a8fa-67d2749a9eab" xlink:to="loc_us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable_019e6c04-3c30-70ca-b756-bf2065a22304" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis_019e6c04-3c30-7494-9b7d-bb9c165dac44" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable_019e6c04-3c30-70ca-b756-bf2065a22304" xlink:to="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis_019e6c04-3c30-7494-9b7d-bb9c165dac44" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AntidilutiveSecuritiesNameDomain_019e6c04-3c30-7494-9b7d-bb9c165dac44_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AntidilutiveSecuritiesNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis_019e6c04-3c30-7494-9b7d-bb9c165dac44" xlink:to="loc_us-gaap_AntidilutiveSecuritiesNameDomain_019e6c04-3c30-7494-9b7d-bb9c165dac44_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AntidilutiveSecuritiesNameDomain_019e6c04-3c30-792a-a1b3-7145a788d7d0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AntidilutiveSecuritiesNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis_019e6c04-3c30-7494-9b7d-bb9c165dac44" xlink:to="loc_us-gaap_AntidilutiveSecuritiesNameDomain_019e6c04-3c30-792a-a1b3-7145a788d7d0" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockCompensationPlanMember_019e6c04-3c30-78aa-b2f1-c349813da49d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockCompensationPlanMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_AntidilutiveSecuritiesNameDomain_019e6c04-3c30-792a-a1b3-7145a788d7d0" xlink:to="loc_us-gaap_StockCompensationPlanMember_019e6c04-3c30-78aa-b2f1-c349813da49d" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_WarrantMember_019e6c04-3c30-77f7-8338-f88c0d8a07a8" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_WarrantMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_AntidilutiveSecuritiesNameDomain_019e6c04-3c30-792a-a1b3-7145a788d7d0" xlink:to="loc_us-gaap_WarrantMember_019e6c04-3c30-77f7-8338-f88c0d8a07a8" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockMember_019e6c04-3c30-731b-b231-b08cb8373c06" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeStockMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_AntidilutiveSecuritiesNameDomain_019e6c04-3c30-792a-a1b3-7145a788d7d0" xlink:to="loc_us-gaap_EmployeeStockMember_019e6c04-3c30-731b-b231-b08cb8373c06" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount_019e6c04-3c30-7d30-ab85-1af10a041064" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems_019e6c04-3c30-7597-a8fa-67d2749a9eab" xlink:to="loc_us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount_019e6c04-3c30-7d30-ab85-1af10a041064" xlink:type="arc" order="0"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/InvestmentsinNonMarketableSecuritiesCarryingValueandFairValueofSecuritiesDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#InvestmentsinNonMarketableSecuritiesCarryingValueandFairValueofSecuritiesDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/InvestmentsinNonMarketableSecuritiesCarryingValueandFairValueofSecuritiesDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_MarketableSecuritiesLineItems_019e6c04-3c30-7a9d-92e8-b8f21fab821b" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_MarketableSecuritiesLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_MarketableSecuritiesTable_019e6c04-3c30-7840-a423-2f4fcd90dde5" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_MarketableSecuritiesTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_MarketableSecuritiesLineItems_019e6c04-3c30-7a9d-92e8-b8f21fab821b" xlink:to="loc_us-gaap_MarketableSecuritiesTable_019e6c04-3c30-7840-a423-2f4fcd90dde5" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_019e6c04-3c30-7fbc-a97a-b306fa553cdf" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SecurityOwnedNotReadilyMarketableAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_MarketableSecuritiesTable_019e6c04-3c30-7840-a423-2f4fcd90dde5" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_019e6c04-3c30-7fbc-a97a-b306fa553cdf" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_019e6c04-3c30-7fbc-a97a-b306fa553cdf_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SecurityOwnedNotReadilyMarketableNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_019e6c04-3c30-7fbc-a97a-b306fa553cdf" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_019e6c04-3c30-7fbc-a97a-b306fa553cdf_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_019e6c04-3c30-75dc-9063-2120f81f5dd0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SecurityOwnedNotReadilyMarketableNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_019e6c04-3c30-7fbc-a97a-b306fa553cdf" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_019e6c04-3c30-75dc-9063-2120f81f5dd0" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_SeqWellMember_019e6c04-3c30-7a64-af37-59abc31ed9db" xlink:href="cdxs-20260630.xsd#cdxs_SeqWellMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_019e6c04-3c30-75dc-9063-2120f81f5dd0" xlink:to="loc_cdxs_SeqWellMember_019e6c04-3c30-7a64-af37-59abc31ed9db" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherAggregatedInvestmentsMember_019e6c04-3c30-788f-ac83-d48bbd7d8074" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherAggregatedInvestmentsMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_019e6c04-3c30-75dc-9063-2120f81f5dd0" xlink:to="loc_us-gaap_OtherAggregatedInvestmentsMember_019e6c04-3c30-788f-ac83-d48bbd7d8074" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueAmount_019e6c04-3c30-7087-85c8-ac9de6ee570c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueAmount"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_MarketableSecuritiesLineItems_019e6c04-3c30-7a9d-92e8-b8f21fab821b" xlink:to="loc_us-gaap_EquitySecuritiesWithoutReadilyDeterminableFairValueAmount_019e6c04-3c30-7087-85c8-ac9de6ee570c" xlink:type="arc" order="0"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/FairValueMeasurementFinancialInstrumentsMeasuredatFairValueonaRecurringBasisDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#FairValueMeasurementFinancialInstrumentsMeasuredatFairValueonaRecurringBasisDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/FairValueMeasurementFinancialInstrumentsMeasuredatFairValueonaRecurringBasisDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_019e6c04-3c30-7d76-9de9-929f7345675c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_019e6c04-3c30-7d76-9de9-929f7345675c" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementOfFinancialPositionLocationBalanceAxis_019e6c04-3c30-7e46-a4fe-c11a24f44c75" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfFinancialPositionLocationBalanceAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_019e6c04-3c30-7d76-9de9-929f7345675c" xlink:to="loc_us-gaap_StatementOfFinancialPositionLocationBalanceAxis_019e6c04-3c30-7e46-a4fe-c11a24f44c75" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueByFairValueHierarchyLevelAxis_019e6c04-3c30-7d31-ae6d-3708db347d22" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_019e6c04-3c30-7d76-9de9-929f7345675c" xlink:to="loc_us-gaap_FairValueByFairValueHierarchyLevelAxis_019e6c04-3c30-7d31-ae6d-3708db347d22" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_019e6c04-3c30-7d31-ae6d-3708db347d22_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_FairValueByFairValueHierarchyLevelAxis_019e6c04-3c30-7d31-ae6d-3708db347d22" xlink:to="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_019e6c04-3c30-7d31-ae6d-3708db347d22_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_019e6c04-3c30-727b-a753-1f40870e9ce5" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_FairValueByFairValueHierarchyLevelAxis_019e6c04-3c30-7d31-ae6d-3708db347d22" xlink:to="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_019e6c04-3c30-727b-a753-1f40870e9ce5" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueInputsLevel1Member_019e6c04-3c30-7a12-84f6-53d3b7b9ed6b" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueInputsLevel1Member"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_019e6c04-3c30-727b-a753-1f40870e9ce5" xlink:to="loc_us-gaap_FairValueInputsLevel1Member_019e6c04-3c30-7a12-84f6-53d3b7b9ed6b" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueInputsLevel2Member_019e6c04-3c30-7ecb-826f-0eda93158167" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueInputsLevel2Member"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_019e6c04-3c30-727b-a753-1f40870e9ce5" xlink:to="loc_us-gaap_FairValueInputsLevel2Member_019e6c04-3c30-7ecb-826f-0eda93158167" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FinancialInstrumentAxis_019e6c04-3c30-7abc-973d-f9ae114fed68" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinancialInstrumentAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_019e6c04-3c30-7d76-9de9-929f7345675c" xlink:to="loc_us-gaap_FinancialInstrumentAxis_019e6c04-3c30-7abc-973d-f9ae114fed68" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7abc-973d-f9ae114fed68_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_FinancialInstrumentAxis_019e6c04-3c30-7abc-973d-f9ae114fed68" xlink:to="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7abc-973d-f9ae114fed68_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7101-8e81-97dc912de396" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_FinancialInstrumentAxis_019e6c04-3c30-7abc-973d-f9ae114fed68" xlink:to="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7101-8e81-97dc912de396" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_MoneyMarketFundsMember_019e6c04-3c30-71dc-b2c0-0e1d86799add" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_MoneyMarketFundsMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7101-8e81-97dc912de396" xlink:to="loc_us-gaap_MoneyMarketFundsMember_019e6c04-3c30-71dc-b2c0-0e1d86799add" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommercialPaperMember_019e6c04-3c30-7dcb-9501-1b9bffe99fca" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommercialPaperMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7101-8e81-97dc912de396" xlink:to="loc_us-gaap_CommercialPaperMember_019e6c04-3c30-7dcb-9501-1b9bffe99fca" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CorporateDebtSecuritiesMember_019e6c04-3c30-7438-9f2c-9e6c77c6efff" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CorporateDebtSecuritiesMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7101-8e81-97dc912de396" xlink:to="loc_us-gaap_CorporateDebtSecuritiesMember_019e6c04-3c30-7438-9f2c-9e6c77c6efff" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_USTreasurySecuritiesMember_019e6c04-3c30-7f74-8585-6dceb216ea53" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_USTreasurySecuritiesMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7101-8e81-97dc912de396" xlink:to="loc_us-gaap_USTreasurySecuritiesMember_019e6c04-3c30-7f74-8585-6dceb216ea53" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_Cash_019e6c04-3c30-791c-a2b7-8b458821b01a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Cash"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_Cash_019e6c04-3c30-791c-a2b7-8b458821b01a" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis_019e6c04-3c30-7ab4-a859-de504d0adda6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis_019e6c04-3c30-7ab4-a859-de504d0adda6" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax_019e6c04-3c30-763b-bbf7-8f2e5fa73ba9" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax_019e6c04-3c30-763b-bbf7-8f2e5fa73ba9" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax_019e6c04-3c30-7916-aeb0-1f5f36306514" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax_019e6c04-3c30-7916-aeb0-1f5f36306514" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_019e6c04-3c30-786e-908c-648377349d80" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_019e6c04-3c30-786e-908c-648377349d80" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CashCashEquivalentsAndShortTermInvestmentsAmortizedCost_019e6c04-3c30-7fd7-a8d6-ca6489ccf003" xlink:href="cdxs-20260630.xsd#cdxs_CashCashEquivalentsAndShortTermInvestmentsAmortizedCost"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_cdxs_CashCashEquivalentsAndShortTermInvestmentsAmortizedCost_019e6c04-3c30-7fd7-a8d6-ca6489ccf003" xlink:type="arc" order="5"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashCashEquivalentsAndShortTermInvestments_019e6c04-3c30-784d-a82b-7081676fbbdc" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashCashEquivalentsAndShortTermInvestments"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_CashCashEquivalentsAndShortTermInvestments_019e6c04-3c30-784d-a82b-7081676fbbdc" xlink:type="arc" order="6"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/FairValueMeasurementFinancialInstrumentsMeasuredatFairValueonaRecurringBasisDetails_1" xlink:type="simple" xlink:href="cdxs-20260630.xsd#FairValueMeasurementFinancialInstrumentsMeasuredatFairValueonaRecurringBasisDetails_1"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/FairValueMeasurementFinancialInstrumentsMeasuredatFairValueonaRecurringBasisDetails_1" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_019e6c04-3c30-7d76-9de9-929f7345675c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_019e6c04-3c30-7d76-9de9-929f7345675c" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueByFairValueHierarchyLevelAxis_019e6c04-3c30-7d31-ae6d-3708db347d22" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_019e6c04-3c30-7d76-9de9-929f7345675c" xlink:to="loc_us-gaap_FairValueByFairValueHierarchyLevelAxis_019e6c04-3c30-7d31-ae6d-3708db347d22" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_019e6c04-3c30-7d31-ae6d-3708db347d22_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_FairValueByFairValueHierarchyLevelAxis_019e6c04-3c30-7d31-ae6d-3708db347d22" xlink:to="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_019e6c04-3c30-7d31-ae6d-3708db347d22_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_019e6c04-3c30-727b-a753-1f40870e9ce5" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_FairValueByFairValueHierarchyLevelAxis_019e6c04-3c30-7d31-ae6d-3708db347d22" xlink:to="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_019e6c04-3c30-727b-a753-1f40870e9ce5" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueInputsLevel1Member_019e6c04-3c30-7a12-84f6-53d3b7b9ed6b" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueInputsLevel1Member"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_019e6c04-3c30-727b-a753-1f40870e9ce5" xlink:to="loc_us-gaap_FairValueInputsLevel1Member_019e6c04-3c30-7a12-84f6-53d3b7b9ed6b" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueInputsLevel2Member_019e6c04-3c30-7ecb-826f-0eda93158167" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueInputsLevel2Member"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueMeasurementsFairValueHierarchyDomain_019e6c04-3c30-727b-a753-1f40870e9ce5" xlink:to="loc_us-gaap_FairValueInputsLevel2Member_019e6c04-3c30-7ecb-826f-0eda93158167" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FinancialInstrumentAxis_019e6c04-3c30-7abc-973d-f9ae114fed68" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinancialInstrumentAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_019e6c04-3c30-7d76-9de9-929f7345675c" xlink:to="loc_us-gaap_FinancialInstrumentAxis_019e6c04-3c30-7abc-973d-f9ae114fed68" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7abc-973d-f9ae114fed68_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_FinancialInstrumentAxis_019e6c04-3c30-7abc-973d-f9ae114fed68" xlink:to="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7abc-973d-f9ae114fed68_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7101-8e81-97dc912de396" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_FinancialInstrumentAxis_019e6c04-3c30-7abc-973d-f9ae114fed68" xlink:to="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7101-8e81-97dc912de396" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_MoneyMarketFundsMember_019e6c04-3c30-71dc-b2c0-0e1d86799add" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_MoneyMarketFundsMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7101-8e81-97dc912de396" xlink:to="loc_us-gaap_MoneyMarketFundsMember_019e6c04-3c30-71dc-b2c0-0e1d86799add" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommercialPaperMember_019e6c04-3c30-7dcb-9501-1b9bffe99fca" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommercialPaperMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7101-8e81-97dc912de396" xlink:to="loc_us-gaap_CommercialPaperMember_019e6c04-3c30-7dcb-9501-1b9bffe99fca" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CorporateDebtSecuritiesMember_019e6c04-3c30-7438-9f2c-9e6c77c6efff" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CorporateDebtSecuritiesMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7101-8e81-97dc912de396" xlink:to="loc_us-gaap_CorporateDebtSecuritiesMember_019e6c04-3c30-7438-9f2c-9e6c77c6efff" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_USTreasurySecuritiesMember_019e6c04-3c30-7f74-8585-6dceb216ea53" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_USTreasurySecuritiesMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_019e6c04-3c30-7101-8e81-97dc912de396" xlink:to="loc_us-gaap_USTreasurySecuritiesMember_019e6c04-3c30-7f74-8585-6dceb216ea53" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_Cash_019e6c04-3c30-791c-a2b7-8b458821b01a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Cash"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_Cash_019e6c04-3c30-791c-a2b7-8b458821b01a" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis_019e6c04-3c30-7ab4-a859-de504d0adda6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis_019e6c04-3c30-7ab4-a859-de504d0adda6" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax_019e6c04-3c30-763b-bbf7-8f2e5fa73ba9" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax_019e6c04-3c30-763b-bbf7-8f2e5fa73ba9" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax_019e6c04-3c30-7916-aeb0-1f5f36306514" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax_019e6c04-3c30-7916-aeb0-1f5f36306514" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_019e6c04-3c30-786e-908c-648377349d80" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_019e6c04-3c30-786e-908c-648377349d80" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CashCashEquivalentsAndShortTermInvestmentsAmortizedCost_019e6c04-3c30-7fd7-a8d6-ca6489ccf003" xlink:href="cdxs-20260630.xsd#cdxs_CashCashEquivalentsAndShortTermInvestmentsAmortizedCost"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_cdxs_CashCashEquivalentsAndShortTermInvestmentsAmortizedCost_019e6c04-3c30-7fd7-a8d6-ca6489ccf003" xlink:type="arc" order="5"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashCashEquivalentsAndShortTermInvestments_019e6c04-3c30-784d-a82b-7081676fbbdc" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashCashEquivalentsAndShortTermInvestments"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-7494-b484-b0353373db26" xlink:to="loc_us-gaap_CashCashEquivalentsAndShortTermInvestments_019e6c04-3c30-784d-a82b-7081676fbbdc" xlink:type="arc" order="6"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/FairValueMeasurementNarrativeDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#FairValueMeasurementNarrativeDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/FairValueMeasurementNarrativeDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-791e-9c4e-de7597d5be61" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_019e6c04-3c30-7089-a26b-67f09c88fcaa" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-791e-9c4e-de7597d5be61" xlink:to="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_019e6c04-3c30-7089-a26b-67f09c88fcaa" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_019e6c04-3c30-70e2-a218-90ff3429c237" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SecurityOwnedNotReadilyMarketableAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable_019e6c04-3c30-7089-a26b-67f09c88fcaa" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_019e6c04-3c30-70e2-a218-90ff3429c237" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_019e6c04-3c30-70e2-a218-90ff3429c237_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SecurityOwnedNotReadilyMarketableNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_019e6c04-3c30-70e2-a218-90ff3429c237" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_019e6c04-3c30-70e2-a218-90ff3429c237_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_019e6c04-3c30-7141-8c00-88cb711aeca4" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SecurityOwnedNotReadilyMarketableNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableAxis_019e6c04-3c30-70e2-a218-90ff3429c237" xlink:to="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_019e6c04-3c30-7141-8c00-88cb711aeca4" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConvertibleDebtMember_019e6c04-3c30-710e-9ccc-d0ad8a1445cb" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConvertibleDebtMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SecurityOwnedNotReadilyMarketableNameDomain_019e6c04-3c30-7141-8c00-88cb711aeca4" xlink:to="loc_us-gaap_ConvertibleDebtMember_019e6c04-3c30-710e-9ccc-d0ad8a1445cb" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtSecuritiesAvailableForSaleAllowanceForCreditLossWriteoff_019e6c04-3c30-7e5c-af02-8db4bd53f83a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtSecuritiesAvailableForSaleAllowanceForCreditLossWriteoff"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-791e-9c4e-de7597d5be61" xlink:to="loc_us-gaap_DebtSecuritiesAvailableForSaleAllowanceForCreditLossWriteoff_019e6c04-3c30-7e5c-af02-8db4bd53f83a" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesGrossUnrealizedLoss_019e6c04-3c30-7e2c-a630-c209a6d36977" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesGrossUnrealizedLoss"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems_019e6c04-3c30-791e-9c4e-de7597d5be61" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesGrossUnrealizedLoss_019e6c04-3c30-7e2c-a630-c209a6d36977" xlink:type="arc" order="1"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/BalanceSheetDetailsPropertyandEquipmentnetDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#BalanceSheetDetailsPropertyandEquipmentnetDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/BalanceSheetDetailsPropertyandEquipmentnetDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentLineItems_019e6c04-3c30-7a7e-b65a-959c72971a05" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_019e6c04-3c30-713c-917f-2150634aed2d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfPropertyPlantAndEquipmentTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_019e6c04-3c30-7a7e-b65a-959c72971a05" xlink:to="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_019e6c04-3c30-713c-917f-2150634aed2d" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_019e6c04-3c30-764d-b890-fbcaa9fb58b5" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentByTypeAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_019e6c04-3c30-713c-917f-2150634aed2d" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_019e6c04-3c30-764d-b890-fbcaa9fb58b5" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-764d-b890-fbcaa9fb58b5_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_019e6c04-3c30-764d-b890-fbcaa9fb58b5" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-764d-b890-fbcaa9fb58b5_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_019e6c04-3c30-764d-b890-fbcaa9fb58b5" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_LaboratoryEquipmentMember_019e6c04-3c30-73cd-ac32-ca7fadba3e9f" xlink:href="cdxs-20260630.xsd#cdxs_LaboratoryEquipmentMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:to="loc_cdxs_LaboratoryEquipmentMember_019e6c04-3c30-73cd-ac32-ca7fadba3e9f" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LeaseholdImprovementsMember_019e6c04-3c30-78bb-86e1-9033ab9db4d8" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LeaseholdImprovementsMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:to="loc_us-gaap_LeaseholdImprovementsMember_019e6c04-3c30-78bb-86e1-9033ab9db4d8" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ComputerEquipmentMember_019e6c04-3c30-73db-968a-1cffa21e6e45" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ComputerEquipmentMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:to="loc_us-gaap_ComputerEquipmentMember_019e6c04-3c30-73db-968a-1cffa21e6e45" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_OfficeEquipmentAndFurnitureMember_019e6c04-3c30-7137-97e4-8098d67f2e85" xlink:href="cdxs-20260630.xsd#cdxs_OfficeEquipmentAndFurnitureMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:to="loc_cdxs_OfficeEquipmentAndFurnitureMember_019e6c04-3c30-7137-97e4-8098d67f2e85" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConstructionInProgressMember_019e6c04-3c30-7504-8b77-90fbe28d9f87" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConstructionInProgressMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:to="loc_us-gaap_ConstructionInProgressMember_019e6c04-3c30-7504-8b77-90fbe28d9f87" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementOfIncomeLocationBalanceAxis_019e6c04-3c30-7134-baf7-01834d0d248f" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfIncomeLocationBalanceAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_019e6c04-3c30-713c-917f-2150634aed2d" xlink:to="loc_us-gaap_StatementOfIncomeLocationBalanceAxis_019e6c04-3c30-7134-baf7-01834d0d248f" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentGross_019e6c04-3c30-705f-bd72-c84a6dc459dd" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentGross"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_019e6c04-3c30-7a7e-b65a-959c72971a05" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentGross_019e6c04-3c30-705f-bd72-c84a6dc459dd" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment_019e6c04-3c30-71ae-be79-8977d452f2e4" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_019e6c04-3c30-7a7e-b65a-959c72971a05" xlink:to="loc_us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment_019e6c04-3c30-71ae-be79-8977d452f2e4" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentNet_019e6c04-3c30-7991-beaf-b5fdc5316624" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentNet"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_019e6c04-3c30-7a7e-b65a-959c72971a05" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentNet_019e6c04-3c30-7991-beaf-b5fdc5316624" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_Depreciation_019e6c04-3c30-7d8c-9d8b-1f06618a9ad3" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Depreciation"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_019e6c04-3c30-7a7e-b65a-959c72971a05" xlink:to="loc_us-gaap_Depreciation_019e6c04-3c30-7d8c-9d8b-1f06618a9ad3" xlink:type="arc" order="3"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/BalanceSheetDetailsPropertyandEquipmentnetDetails_1" xlink:type="simple" xlink:href="cdxs-20260630.xsd#BalanceSheetDetailsPropertyandEquipmentnetDetails_1"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/BalanceSheetDetailsPropertyandEquipmentnetDetails_1" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentLineItems_019e6c04-3c30-7a7e-b65a-959c72971a05" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_019e6c04-3c30-713c-917f-2150634aed2d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfPropertyPlantAndEquipmentTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_019e6c04-3c30-7a7e-b65a-959c72971a05" xlink:to="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_019e6c04-3c30-713c-917f-2150634aed2d" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_019e6c04-3c30-764d-b890-fbcaa9fb58b5" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentByTypeAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfPropertyPlantAndEquipmentTable_019e6c04-3c30-713c-917f-2150634aed2d" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_019e6c04-3c30-764d-b890-fbcaa9fb58b5" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-764d-b890-fbcaa9fb58b5_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_019e6c04-3c30-764d-b890-fbcaa9fb58b5" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-764d-b890-fbcaa9fb58b5_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentByTypeAxis_019e6c04-3c30-764d-b890-fbcaa9fb58b5" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_LaboratoryEquipmentMember_019e6c04-3c30-73cd-ac32-ca7fadba3e9f" xlink:href="cdxs-20260630.xsd#cdxs_LaboratoryEquipmentMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:to="loc_cdxs_LaboratoryEquipmentMember_019e6c04-3c30-73cd-ac32-ca7fadba3e9f" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LeaseholdImprovementsMember_019e6c04-3c30-78bb-86e1-9033ab9db4d8" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LeaseholdImprovementsMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:to="loc_us-gaap_LeaseholdImprovementsMember_019e6c04-3c30-78bb-86e1-9033ab9db4d8" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ComputerEquipmentMember_019e6c04-3c30-73db-968a-1cffa21e6e45" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ComputerEquipmentMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:to="loc_us-gaap_ComputerEquipmentMember_019e6c04-3c30-73db-968a-1cffa21e6e45" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_OfficeEquipmentAndFurnitureMember_019e6c04-3c30-7137-97e4-8098d67f2e85" xlink:href="cdxs-20260630.xsd#cdxs_OfficeEquipmentAndFurnitureMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:to="loc_cdxs_OfficeEquipmentAndFurnitureMember_019e6c04-3c30-7137-97e4-8098d67f2e85" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConstructionInProgressMember_019e6c04-3c30-7504-8b77-90fbe28d9f87" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConstructionInProgressMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentTypeDomain_019e6c04-3c30-7f46-aa90-ac8fcc8de8a1" xlink:to="loc_us-gaap_ConstructionInProgressMember_019e6c04-3c30-7504-8b77-90fbe28d9f87" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentGross_019e6c04-3c30-705f-bd72-c84a6dc459dd" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentGross"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_019e6c04-3c30-7a7e-b65a-959c72971a05" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentGross_019e6c04-3c30-705f-bd72-c84a6dc459dd" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment_019e6c04-3c30-71ae-be79-8977d452f2e4" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_019e6c04-3c30-7a7e-b65a-959c72971a05" xlink:to="loc_us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment_019e6c04-3c30-71ae-be79-8977d452f2e4" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentNet_019e6c04-3c30-7991-beaf-b5fdc5316624" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentNet"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_019e6c04-3c30-7a7e-b65a-959c72971a05" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentNet_019e6c04-3c30-7991-beaf-b5fdc5316624" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_Depreciation_019e6c04-3c30-7d8c-9d8b-1f06618a9ad3" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Depreciation"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_PropertyPlantAndEquipmentLineItems_019e6c04-3c30-7a7e-b65a-959c72971a05" xlink:to="loc_us-gaap_Depreciation_019e6c04-3c30-7d8c-9d8b-1f06618a9ad3" xlink:type="arc" order="3"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/StockbasedCompensationNarrativeDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#StockbasedCompensationNarrativeDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/StockbasedCompensationNarrativeDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_019e6c04-3cf7-7508-8d08-dfc4e1273141" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_019e6c04-3cf7-7b20-bbf3-5fe08bb42bdc" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_019e6c04-3cf7-7508-8d08-dfc4e1273141" xlink:to="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_019e6c04-3cf7-7b20-bbf3-5fe08bb42bdc" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AwardTypeAxis_019e6c04-3cf7-7ea5-8872-23f92461db61" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AwardTypeAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable_019e6c04-3cf7-7b20-bbf3-5fe08bb42bdc" xlink:to="loc_us-gaap_AwardTypeAxis_019e6c04-3cf7-7ea5-8872-23f92461db61" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7ea5-8872-23f92461db61_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_AwardTypeAxis_019e6c04-3cf7-7ea5-8872-23f92461db61" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7ea5-8872-23f92461db61_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a0a-8d8b-9aa032d789d6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_AwardTypeAxis_019e6c04-3cf7-7ea5-8872-23f92461db61" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a0a-8d8b-9aa032d789d6" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockMember_019e6c04-3cf7-71bd-a384-9456fc03d9eb" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeStockMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a0a-8d8b-9aa032d789d6" xlink:to="loc_us-gaap_EmployeeStockMember_019e6c04-3cf7-71bd-a384-9456fc03d9eb" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockOptionMember_019e6c04-3cf7-7c2d-9359-c6c935d0bc1a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeStockOptionMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a0a-8d8b-9aa032d789d6" xlink:to="loc_us-gaap_EmployeeStockOptionMember_019e6c04-3cf7-7c2d-9359-c6c935d0bc1a" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedStockUnitsRSUMember_019e6c04-3cf7-7419-8ed5-a41379fd29ae" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RestrictedStockUnitsRSUMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a0a-8d8b-9aa032d789d6" xlink:to="loc_us-gaap_RestrictedStockUnitsRSUMember_019e6c04-3cf7-7419-8ed5-a41379fd29ae" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardSharesIssuedInPeriod_019e6c04-3cf7-7260-b0ad-aabd00992943" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardSharesIssuedInPeriod"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_019e6c04-3cf7-7508-8d08-dfc4e1273141" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardSharesIssuedInPeriod_019e6c04-3cf7-7260-b0ad-aabd00992943" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommonStockCapitalSharesReservedForFutureIssuance_019e6c04-3cf7-787f-991b-b9915f2505a2" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommonStockCapitalSharesReservedForFutureIssuance"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_019e6c04-3cf7-7508-8d08-dfc4e1273141" xlink:to="loc_us-gaap_CommonStockCapitalSharesReservedForFutureIssuance_019e6c04-3cf7-787f-991b-b9915f2505a2" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensation_019e6c04-3cf7-7112-909c-4a299897c609" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensation"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_019e6c04-3cf7-7508-8d08-dfc4e1273141" xlink:to="loc_us-gaap_ShareBasedCompensation_019e6c04-3cf7-7112-909c-4a299897c609" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognized_019e6c04-3cf7-751f-a256-a5997a99912a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognized"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_019e6c04-3cf7-7508-8d08-dfc4e1273141" xlink:to="loc_us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognized_019e6c04-3cf7-751f-a256-a5997a99912a" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions_019e6c04-3cf7-740b-89de-5c925f251831" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_019e6c04-3cf7-7508-8d08-dfc4e1273141" xlink:to="loc_us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions_019e6c04-3cf7-740b-89de-5c925f251831" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedShareBasedAwardsOtherThanOptions_019e6c04-3cf7-7e3f-880d-2fbcc4b33526" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedShareBasedAwardsOtherThanOptions"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems_019e6c04-3cf7-7508-8d08-dfc4e1273141" xlink:to="loc_us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedShareBasedAwardsOtherThanOptions_019e6c04-3cf7-7e3f-880d-2fbcc4b33526" xlink:type="arc" order="5"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/StockbasedCompensationStockbasedCompensationExpenseDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#StockbasedCompensationStockbasedCompensationExpenseDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/StockbasedCompensationStockbasedCompensationExpenseDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems_019e6c04-3cf7-7efa-b929-264bd7679eb0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable_019e6c04-3cf7-75d9-bd42-17da66f1bc95" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems_019e6c04-3cf7-7efa-b929-264bd7679eb0" xlink:to="loc_us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable_019e6c04-3cf7-75d9-bd42-17da66f1bc95" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StatementOfIncomeLocationBalanceAxis_019e6c04-3cf7-71c0-812e-c1fdca52d4c6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StatementOfIncomeLocationBalanceAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable_019e6c04-3cf7-75d9-bd42-17da66f1bc95" xlink:to="loc_us-gaap_StatementOfIncomeLocationBalanceAxis_019e6c04-3cf7-71c0-812e-c1fdca52d4c6" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AwardTypeAxis_019e6c04-3cf7-7e60-8c9d-08bc0a3730ab" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AwardTypeAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable_019e6c04-3cf7-75d9-bd42-17da66f1bc95" xlink:to="loc_us-gaap_AwardTypeAxis_019e6c04-3cf7-7e60-8c9d-08bc0a3730ab" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7e60-8c9d-08bc0a3730ab_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_AwardTypeAxis_019e6c04-3cf7-7e60-8c9d-08bc0a3730ab" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7e60-8c9d-08bc0a3730ab_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a74-9159-886049ad637c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_AwardTypeAxis_019e6c04-3cf7-7e60-8c9d-08bc0a3730ab" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a74-9159-886049ad637c" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockOptionMember_019e6c04-3cf7-7d88-9013-2107ff0bd44d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeStockOptionMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a74-9159-886049ad637c" xlink:to="loc_us-gaap_EmployeeStockOptionMember_019e6c04-3cf7-7d88-9013-2107ff0bd44d" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_RSAsandRSUsMember_019e6c04-3cf7-7d55-8558-520ea3ce3f10" xlink:href="cdxs-20260630.xsd#cdxs_RSAsandRSUsMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a74-9159-886049ad637c" xlink:to="loc_cdxs_RSAsandRSUsMember_019e6c04-3cf7-7d55-8558-520ea3ce3f10" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockMember_019e6c04-3cf7-7375-8224-0127ae22ca72" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeStockMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a74-9159-886049ad637c" xlink:to="loc_us-gaap_EmployeeStockMember_019e6c04-3cf7-7375-8224-0127ae22ca72" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensation_019e6c04-3cf7-75f3-8e4b-d97abbfffc53" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensation"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems_019e6c04-3cf7-7efa-b929-264bd7679eb0" xlink:to="loc_us-gaap_ShareBasedCompensation_019e6c04-3cf7-75f3-8e4b-d97abbfffc53" xlink:type="arc" order="0"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/StockbasedCompensationStockbasedCompensationExpenseDetails_1" xlink:type="simple" xlink:href="cdxs-20260630.xsd#StockbasedCompensationStockbasedCompensationExpenseDetails_1"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/StockbasedCompensationStockbasedCompensationExpenseDetails_1" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems_019e6c04-3cf7-7efa-b929-264bd7679eb0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable_019e6c04-3cf7-75d9-bd42-17da66f1bc95" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems_019e6c04-3cf7-7efa-b929-264bd7679eb0" xlink:to="loc_us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable_019e6c04-3cf7-75d9-bd42-17da66f1bc95" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AwardTypeAxis_019e6c04-3cf7-7e60-8c9d-08bc0a3730ab" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AwardTypeAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable_019e6c04-3cf7-75d9-bd42-17da66f1bc95" xlink:to="loc_us-gaap_AwardTypeAxis_019e6c04-3cf7-7e60-8c9d-08bc0a3730ab" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7e60-8c9d-08bc0a3730ab_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_AwardTypeAxis_019e6c04-3cf7-7e60-8c9d-08bc0a3730ab" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7e60-8c9d-08bc0a3730ab_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a74-9159-886049ad637c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_AwardTypeAxis_019e6c04-3cf7-7e60-8c9d-08bc0a3730ab" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a74-9159-886049ad637c" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockOptionMember_019e6c04-3cf7-7d88-9013-2107ff0bd44d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeStockOptionMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a74-9159-886049ad637c" xlink:to="loc_us-gaap_EmployeeStockOptionMember_019e6c04-3cf7-7d88-9013-2107ff0bd44d" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_RSAsandRSUsMember_019e6c04-3cf7-7d55-8558-520ea3ce3f10" xlink:href="cdxs-20260630.xsd#cdxs_RSAsandRSUsMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a74-9159-886049ad637c" xlink:to="loc_cdxs_RSAsandRSUsMember_019e6c04-3cf7-7d55-8558-520ea3ce3f10" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeStockMember_019e6c04-3cf7-7375-8224-0127ae22ca72" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeStockMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_019e6c04-3cf7-7a74-9159-886049ad637c" xlink:to="loc_us-gaap_EmployeeStockMember_019e6c04-3cf7-7375-8224-0127ae22ca72" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensation_019e6c04-3cf7-75f3-8e4b-d97abbfffc53" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensation"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems_019e6c04-3cf7-7efa-b929-264bd7679eb0" xlink:to="loc_us-gaap_ShareBasedCompensation_019e6c04-3cf7-75f3-8e4b-d97abbfffc53" xlink:type="arc" order="0"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/CapitalStockDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#CapitalStockDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/CapitalStockDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfStockLineItems_019e6c04-3cf7-7374-afa7-ad275014cdaf" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ClassOfStockLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfStockByClassTable_019e6c04-3cf7-7cc1-9b4d-a5df37e80bac" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfStockByClassTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_ClassOfStockLineItems_019e6c04-3cf7-7374-afa7-ad275014cdaf" xlink:to="loc_us-gaap_ScheduleOfStockByClassTable_019e6c04-3cf7-7cc1-9b4d-a5df37e80bac" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsidiarySaleOfStockAxis_019e6c04-3cf7-72db-93fc-e55406473125" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsidiarySaleOfStockAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfStockByClassTable_019e6c04-3cf7-7cc1-9b4d-a5df37e80bac" xlink:to="loc_us-gaap_SubsidiarySaleOfStockAxis_019e6c04-3cf7-72db-93fc-e55406473125" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SaleOfStockNameOfTransactionDomain_019e6c04-3cf7-72db-93fc-e55406473125_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_SubsidiarySaleOfStockAxis_019e6c04-3cf7-72db-93fc-e55406473125" xlink:to="loc_us-gaap_SaleOfStockNameOfTransactionDomain_019e6c04-3cf7-72db-93fc-e55406473125_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SaleOfStockNameOfTransactionDomain_019e6c04-3cf7-73e6-a417-318165c95a48" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_SubsidiarySaleOfStockAxis_019e6c04-3cf7-72db-93fc-e55406473125" xlink:to="loc_us-gaap_SaleOfStockNameOfTransactionDomain_019e6c04-3cf7-73e6-a417-318165c95a48" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CantorSalesAgreementMember_019e6c04-3cf7-74ca-8631-149abfa81496" xlink:href="cdxs-20260630.xsd#cdxs_CantorSalesAgreementMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SaleOfStockNameOfTransactionDomain_019e6c04-3cf7-73e6-a417-318165c95a48" xlink:to="loc_cdxs_CantorSalesAgreementMember_019e6c04-3cf7-74ca-8631-149abfa81496" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_LegalEntityAxis_019e6c04-3cf7-7e2c-8f97-d8785c675ee0" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_LegalEntityAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfStockByClassTable_019e6c04-3cf7-7cc1-9b4d-a5df37e80bac" xlink:to="loc_dei_LegalEntityAxis_019e6c04-3cf7-7e2c-8f97-d8785c675ee0" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityDomain_019e6c04-3cf7-7e2c-8f97-d8785c675ee0_default" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_dei_LegalEntityAxis_019e6c04-3cf7-7e2c-8f97-d8785c675ee0" xlink:to="loc_dei_EntityDomain_019e6c04-3cf7-7e2c-8f97-d8785c675ee0_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityDomain_019e6c04-3cf7-7a16-8307-84c9503c2918" xlink:href="https://xbrl.sec.gov/dei/2026/dei-2026.xsd#dei_EntityDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_dei_LegalEntityAxis_019e6c04-3cf7-7e2c-8f97-d8785c675ee0" xlink:to="loc_dei_EntityDomain_019e6c04-3cf7-7a16-8307-84c9503c2918" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CantorMember_019e6c04-3cf7-7b67-b452-f573ee9785a3" xlink:href="cdxs-20260630.xsd#cdxs_CantorMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_dei_EntityDomain_019e6c04-3cf7-7a16-8307-84c9503c2918" xlink:to="loc_cdxs_CantorMember_019e6c04-3cf7-7b67-b452-f573ee9785a3" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeAxis_019f87fb-cac5-76eb-b2b9-1b9bd7926617" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventTypeAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfStockByClassTable_019e6c04-3cf7-7cc1-9b4d-a5df37e80bac" xlink:to="loc_us-gaap_SubsequentEventTypeAxis_019f87fb-cac5-76eb-b2b9-1b9bd7926617" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeDomain_019f87fb-cac5-76eb-b2b9-1b9bd7926617_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_SubsequentEventTypeAxis_019f87fb-cac5-76eb-b2b9-1b9bd7926617" xlink:to="loc_us-gaap_SubsequentEventTypeDomain_019f87fb-cac5-76eb-b2b9-1b9bd7926617_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeDomain_019f87fb-cac5-7f8b-b3cd-8b8e24f3cf40" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_SubsequentEventTypeAxis_019f87fb-cac5-76eb-b2b9-1b9bd7926617" xlink:to="loc_us-gaap_SubsequentEventTypeDomain_019f87fb-cac5-7f8b-b3cd-8b8e24f3cf40" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventMember_019f87fc-07e9-7507-87fa-792ab21393c4" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventTypeDomain_019f87fb-cac5-7f8b-b3cd-8b8e24f3cf40" xlink:to="loc_us-gaap_SubsequentEventMember_019f87fc-07e9-7507-87fa-792ab21393c4" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised_019e6c04-3cf7-7a5c-a858-7a5e2f7e529e" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_019e6c04-3cf7-7374-afa7-ad275014cdaf" xlink:to="loc_us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised_019e6c04-3cf7-7a5c-a858-7a5e2f7e529e" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsExercisesInPeriodWeightedAverageExercisePrice_019e6c04-3cf7-778a-ba8d-ea8f481be0be" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsExercisesInPeriodWeightedAverageExercisePrice"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_019e6c04-3cf7-7374-afa7-ad275014cdaf" xlink:to="loc_us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsExercisesInPeriodWeightedAverageExercisePrice_019e6c04-3cf7-778a-ba8d-ea8f481be0be" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_NetProceedsFromStockOptionsExercised_019e6c04-3cf7-7ac5-9410-92539f01b09d" xlink:href="cdxs-20260630.xsd#cdxs_NetProceedsFromStockOptionsExercised"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_019e6c04-3cf7-7374-afa7-ad275014cdaf" xlink:to="loc_cdxs_NetProceedsFromStockOptionsExercised_019e6c04-3cf7-7ac5-9410-92539f01b09d" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SaleOfStockConsiderationReceivedOnTransaction_019e6c04-3cf7-72d9-8ad0-44992a8312f8" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SaleOfStockConsiderationReceivedOnTransaction"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_019e6c04-3cf7-7374-afa7-ad275014cdaf" xlink:to="loc_us-gaap_SaleOfStockConsiderationReceivedOnTransaction_019e6c04-3cf7-72d9-8ad0-44992a8312f8" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_SaleOfStockCommissionFeePercent_019e6c04-3cf7-7a53-8d79-2751eb6732f2" xlink:href="cdxs-20260630.xsd#cdxs_SaleOfStockCommissionFeePercent"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_019e6c04-3cf7-7374-afa7-ad275014cdaf" xlink:to="loc_cdxs_SaleOfStockCommissionFeePercent_019e6c04-3cf7-7a53-8d79-2751eb6732f2" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockIssuedDuringPeriodSharesNewIssues_019e6c04-3cf7-7be1-bbbd-06567d2ed054" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_019e6c04-3cf7-7374-afa7-ad275014cdaf" xlink:to="loc_us-gaap_StockIssuedDuringPeriodSharesNewIssues_019e6c04-3cf7-7be1-bbbd-06567d2ed054" xlink:type="arc" order="5"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_SaleOfStockConsiderationReceivedOnTransactionNet_019e6c04-3cf7-772a-ab0b-0378de255b89" xlink:href="cdxs-20260630.xsd#cdxs_SaleOfStockConsiderationReceivedOnTransactionNet"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_019e6c04-3cf7-7374-afa7-ad275014cdaf" xlink:to="loc_cdxs_SaleOfStockConsiderationReceivedOnTransactionNet_019e6c04-3cf7-772a-ab0b-0378de255b89" xlink:type="arc" order="6"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_SaleOfStockValueOfSharesForIssuance_019e6c04-3cf7-7c1a-9749-fd0a3f081f11" xlink:href="cdxs-20260630.xsd#cdxs_SaleOfStockValueOfSharesForIssuance"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfStockLineItems_019e6c04-3cf7-7374-afa7-ad275014cdaf" xlink:to="loc_cdxs_SaleOfStockValueOfSharesForIssuance_019e6c04-3cf7-7c1a-9749-fd0a3f081f11" xlink:type="arc" order="7"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/CommitmentsandContingenciesNarrativeDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#CommitmentsandContingenciesNarrativeDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/CommitmentsandContingenciesNarrativeDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitmentsLineItems_019e6c04-3cf7-74c1-90b8-a56034aacdbf" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherCommitmentsLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitmentsTable_019e6c04-3cf7-7897-af09-3965c0a92d0b" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherCommitmentsTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_OtherCommitmentsLineItems_019e6c04-3cf7-74c1-90b8-a56034aacdbf" xlink:to="loc_us-gaap_OtherCommitmentsTable_019e6c04-3cf7-7897-af09-3965c0a92d0b" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LossContingenciesByNatureOfContingencyAxis_019e6c04-3cf7-739a-8649-0d98bbdb0342" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LossContingenciesByNatureOfContingencyAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_OtherCommitmentsTable_019e6c04-3cf7-7897-af09-3965c0a92d0b" xlink:to="loc_us-gaap_LossContingenciesByNatureOfContingencyAxis_019e6c04-3cf7-739a-8649-0d98bbdb0342" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LossContingencyNatureDomain_019e6c04-3cf7-739a-8649-0d98bbdb0342_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LossContingencyNatureDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_LossContingenciesByNatureOfContingencyAxis_019e6c04-3cf7-739a-8649-0d98bbdb0342" xlink:to="loc_us-gaap_LossContingencyNatureDomain_019e6c04-3cf7-739a-8649-0d98bbdb0342_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LossContingencyNatureDomain_019e6c04-3cf7-7fa8-b4a6-87673add8a6a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LossContingencyNatureDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_LossContingenciesByNatureOfContingencyAxis_019e6c04-3cf7-739a-8649-0d98bbdb0342" xlink:to="loc_us-gaap_LossContingencyNatureDomain_019e6c04-3cf7-7fa8-b4a6-87673add8a6a" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_IndemnificationGuaranteeMember_019e6c04-3cf7-72f9-8626-fbdc8ef64e07" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IndemnificationGuaranteeMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LossContingencyNatureDomain_019e6c04-3cf7-7fa8-b4a6-87673add8a6a" xlink:to="loc_us-gaap_IndemnificationGuaranteeMember_019e6c04-3cf7-72f9-8626-fbdc8ef64e07" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LossContingencyAccrualCarryingValueCurrent_019e6c04-3cf7-7a5c-8f23-245864a69aa8" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LossContingencyAccrualCarryingValueCurrent"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_OtherCommitmentsLineItems_019e6c04-3cf7-74c1-90b8-a56034aacdbf" xlink:to="loc_us-gaap_LossContingencyAccrualCarryingValueCurrent_019e6c04-3cf7-7a5c-8f23-245864a69aa8" xlink:type="arc" order="0"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/DebtNarrativeDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#DebtNarrativeDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/DebtNarrativeDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentTable_019e6c04-3cf7-73bc-bf6c-4998adfea525" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_us-gaap_DebtInstrumentTable_019e6c04-3cf7-73bc-bf6c-4998adfea525" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentAxis_019e6c04-3cf7-7404-bc3c-519db23a81a5" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DebtInstrumentTable_019e6c04-3cf7-73bc-bf6c-4998adfea525" xlink:to="loc_us-gaap_DebtInstrumentAxis_019e6c04-3cf7-7404-bc3c-519db23a81a5" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentNameDomain_019e6c04-3cf7-7404-bc3c-519db23a81a5_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_DebtInstrumentAxis_019e6c04-3cf7-7404-bc3c-519db23a81a5" xlink:to="loc_us-gaap_DebtInstrumentNameDomain_019e6c04-3cf7-7404-bc3c-519db23a81a5_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentNameDomain_019e6c04-3cf7-7382-9191-50d3055e7224" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentNameDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_DebtInstrumentAxis_019e6c04-3cf7-7404-bc3c-519db23a81a5" xlink:to="loc_us-gaap_DebtInstrumentNameDomain_019e6c04-3cf7-7382-9191-50d3055e7224" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_InnovatusLoanMember_019e6c04-3cf7-7a44-a30f-c678fbc1878f" xlink:href="cdxs-20260630.xsd#cdxs_InnovatusLoanMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentNameDomain_019e6c04-3cf7-7382-9191-50d3055e7224" xlink:to="loc_cdxs_InnovatusLoanMember_019e6c04-3cf7-7a44-a30f-c678fbc1878f" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_InnovatusLoanFirstTrancheMember_019e6c04-3cf7-718d-a0d4-8672c842ed0b" xlink:href="cdxs-20260630.xsd#cdxs_InnovatusLoanFirstTrancheMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentNameDomain_019e6c04-3cf7-7382-9191-50d3055e7224" xlink:to="loc_cdxs_InnovatusLoanFirstTrancheMember_019e6c04-3cf7-718d-a0d4-8672c842ed0b" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_InnovatusLoanSecondTrancheMember_019e6c04-3cf7-7a9b-9d10-bf53dc4f806a" xlink:href="cdxs-20260630.xsd#cdxs_InnovatusLoanSecondTrancheMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentNameDomain_019e6c04-3cf7-7382-9191-50d3055e7224" xlink:to="loc_cdxs_InnovatusLoanSecondTrancheMember_019e6c04-3cf7-7a9b-9d10-bf53dc4f806a" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_TermLoanMember_019e6c04-3cf7-7c47-afa2-934cb6e23e6d" xlink:href="cdxs-20260630.xsd#cdxs_TermLoanMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentNameDomain_019e6c04-3cf7-7382-9191-50d3055e7224" xlink:to="loc_cdxs_TermLoanMember_019e6c04-3cf7-7c47-afa2-934cb6e23e6d" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LongtermDebtTypeAxis_019e6c04-3cf7-79df-9acd-a653d7a976b8" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LongtermDebtTypeAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DebtInstrumentTable_019e6c04-3cf7-73bc-bf6c-4998adfea525" xlink:to="loc_us-gaap_LongtermDebtTypeAxis_019e6c04-3cf7-79df-9acd-a653d7a976b8" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LongtermDebtTypeDomain_019e6c04-3cf7-79df-9acd-a653d7a976b8_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LongtermDebtTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_LongtermDebtTypeAxis_019e6c04-3cf7-79df-9acd-a653d7a976b8" xlink:to="loc_us-gaap_LongtermDebtTypeDomain_019e6c04-3cf7-79df-9acd-a653d7a976b8_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LongtermDebtTypeDomain_019e6c04-3cf7-7cb0-a905-b753ee24437b" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LongtermDebtTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_LongtermDebtTypeAxis_019e6c04-3cf7-79df-9acd-a653d7a976b8" xlink:to="loc_us-gaap_LongtermDebtTypeDomain_019e6c04-3cf7-7cb0-a905-b753ee24437b" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SecuredDebtMember_019e6c04-3cf7-7b27-855e-a89e9715cf5b" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SecuredDebtMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_LongtermDebtTypeDomain_019e6c04-3cf7-7cb0-a905-b753ee24437b" xlink:to="loc_us-gaap_SecuredDebtMember_019e6c04-3cf7-7b27-855e-a89e9715cf5b" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_RangeAxis_019e6c04-3cf7-7ff9-a237-9f6a8c106d9f" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DebtInstrumentTable_019e6c04-3cf7-73bc-bf6c-4998adfea525" xlink:to="loc_srt_RangeAxis_019e6c04-3cf7-7ff9-a237-9f6a8c106d9f" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_RangeMember_019e6c04-3cf7-7ff9-a237-9f6a8c106d9f_default" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_RangeAxis_019e6c04-3cf7-7ff9-a237-9f6a8c106d9f" xlink:to="loc_srt_RangeMember_019e6c04-3cf7-7ff9-a237-9f6a8c106d9f_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_RangeMember_019e6c04-3cf7-7ae5-97d1-a76a00e152c5" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_RangeMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_RangeAxis_019e6c04-3cf7-7ff9-a237-9f6a8c106d9f" xlink:to="loc_srt_RangeMember_019e6c04-3cf7-7ae5-97d1-a76a00e152c5" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_MaximumMember_019e6c04-3cf7-72eb-9315-8735893d7b79" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_MaximumMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RangeMember_019e6c04-3cf7-7ae5-97d1-a76a00e152c5" xlink:to="loc_srt_MaximumMember_019e6c04-3cf7-72eb-9315-8735893d7b79" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_MinimumMember_019e6c04-3cf7-759e-8a35-447a687b2a80" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_MinimumMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_RangeMember_019e6c04-3cf7-7ae5-97d1-a76a00e152c5" xlink:to="loc_srt_MinimumMember_019e6c04-3cf7-759e-8a35-447a687b2a80" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfWarrantOrRightAxis_019e6c04-3cf7-7f8f-806a-81cbe4baa39e" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ClassOfWarrantOrRightAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_DebtInstrumentTable_019e6c04-3cf7-73bc-bf6c-4998adfea525" xlink:to="loc_us-gaap_ClassOfWarrantOrRightAxis_019e6c04-3cf7-7f8f-806a-81cbe4baa39e" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfWarrantOrRightDomain_019e6c04-3cf7-7f8f-806a-81cbe4baa39e_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ClassOfWarrantOrRightDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ClassOfWarrantOrRightAxis_019e6c04-3cf7-7f8f-806a-81cbe4baa39e" xlink:to="loc_us-gaap_ClassOfWarrantOrRightDomain_019e6c04-3cf7-7f8f-806a-81cbe4baa39e_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfWarrantOrRightDomain_019e6c04-3cf7-7430-82a7-567eb096f62a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ClassOfWarrantOrRightDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ClassOfWarrantOrRightAxis_019e6c04-3cf7-7f8f-806a-81cbe4baa39e" xlink:to="loc_us-gaap_ClassOfWarrantOrRightDomain_019e6c04-3cf7-7430-82a7-567eb096f62a" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_InnovatusLoanWarrantsMember_019e6c04-3cf7-7f7c-aecf-9453d5571ec1" xlink:href="cdxs-20260630.xsd#cdxs_InnovatusLoanWarrantsMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ClassOfWarrantOrRightDomain_019e6c04-3cf7-7430-82a7-567eb096f62a" xlink:to="loc_cdxs_InnovatusLoanWarrantsMember_019e6c04-3cf7-7f7c-aecf-9453d5571ec1" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentTerm_019e6c04-3cf7-7651-aa10-4990d2f70962" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentTerm"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_us-gaap_DebtInstrumentTerm_019e6c04-3cf7-7651-aa10-4990d2f70962" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentFaceAmount_019e6c04-3cf7-706a-9dd1-f9dbb2eda8d8" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentFaceAmount"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_us-gaap_DebtInstrumentFaceAmount_019e6c04-3cf7-706a-9dd1-f9dbb2eda8d8" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_DebtInstrumentNumberOfTranches_019e6c04-3cf7-7f41-a242-d3bfda93d2eb" xlink:href="cdxs-20260630.xsd#cdxs_DebtInstrumentNumberOfTranches"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_cdxs_DebtInstrumentNumberOfTranches_019e6c04-3cf7-7f41-a242-d3bfda93d2eb" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_DebtInstrumentFacilityFeePercent_019e6c04-3cf7-7a48-87b3-ebe97d6438ee" xlink:href="cdxs-20260630.xsd#cdxs_DebtInstrumentFacilityFeePercent"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_cdxs_DebtInstrumentFacilityFeePercent_019e6c04-3cf7-7a48-87b3-ebe97d6438ee" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_InvestmentVariableInterestRateTypeExtensibleEnumeration_019e6c04-3cf7-7349-be5e-0fd1db370a3d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InvestmentVariableInterestRateTypeExtensibleEnumeration"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_us-gaap_InvestmentVariableInterestRateTypeExtensibleEnumeration_019e6c04-3cf7-7349-be5e-0fd1db370a3d" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentInterestRateStatedPercentage_019e6c04-3cf7-7916-bad9-b76db80fc298" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_us-gaap_DebtInstrumentInterestRateStatedPercentage_019e6c04-3cf7-7916-bad9-b76db80fc298" xlink:type="arc" order="5"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentBasisSpreadOnVariableRate1_019e6c04-3cf7-78dd-b68b-71ffd87f1ac3" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentBasisSpreadOnVariableRate1"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_us-gaap_DebtInstrumentBasisSpreadOnVariableRate1_019e6c04-3cf7-78dd-b68b-71ffd87f1ac3" xlink:type="arc" order="6"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_DebtInstrumentInterestPaidInKind_019e6c04-3cf7-7118-a5af-3634acebe9e8" xlink:href="cdxs-20260630.xsd#cdxs_DebtInstrumentInterestPaidInKind"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_cdxs_DebtInstrumentInterestPaidInKind_019e6c04-3cf7-7118-a5af-3634acebe9e8" xlink:type="arc" order="7"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_DebtInstrumentInterestPayableTerm_019e6c04-3cf7-786c-a116-7998fe407881" xlink:href="cdxs-20260630.xsd#cdxs_DebtInstrumentInterestPayableTerm"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_cdxs_DebtInstrumentInterestPayableTerm_019e6c04-3cf7-786c-a116-7998fe407881" xlink:type="arc" order="8"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_EarlyRepaymentFeePercentage_019e6c04-3cf7-7d50-b940-209037947306" xlink:href="cdxs-20260630.xsd#cdxs_EarlyRepaymentFeePercentage"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_cdxs_EarlyRepaymentFeePercentage_019e6c04-3cf7-7d50-b940-209037947306" xlink:type="arc" order="9"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_DebtInstrumentExitFeePercent_019e6c04-3cf7-73fe-ba39-816e5174c0ed" xlink:href="cdxs-20260630.xsd#cdxs_DebtInstrumentExitFeePercent"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_cdxs_DebtInstrumentExitFeePercent_019e6c04-3cf7-73fe-ba39-816e5174c0ed" xlink:type="arc" order="10"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentUnamortizedDiscount_019e6c04-3cf7-701a-a5a5-6ebe94f6040c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentUnamortizedDiscount"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_us-gaap_DebtInstrumentUnamortizedDiscount_019e6c04-3cf7-701a-a5a5-6ebe94f6040c" xlink:type="arc" order="11"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_UnamortizedDebtIssuanceExpense_019e6c04-3cf7-7e48-9ad8-23fdc98bc9bf" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_UnamortizedDebtIssuanceExpense"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_us-gaap_UnamortizedDebtIssuanceExpense_019e6c04-3cf7-7e48-9ad8-23fdc98bc9bf" xlink:type="arc" order="12"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_InterestExpenseDebt_019e6c04-3cf7-7f2f-b917-60becfd04754" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InterestExpenseDebt"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_us-gaap_InterestExpenseDebt_019e6c04-3cf7-7f2f-b917-60becfd04754" xlink:type="arc" order="13"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DebtInstrumentInterestRateEffectivePercentage_019e6c04-3cf7-70f4-9956-16974e2727dd" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DebtInstrumentInterestRateEffectivePercentage"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_us-gaap_DebtInstrumentInterestRateEffectivePercentage_019e6c04-3cf7-70f4-9956-16974e2727dd" xlink:type="arc" order="14"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights_019e6c04-3cf7-7424-ba5e-89ec4076004d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights_019e6c04-3cf7-7424-ba5e-89ec4076004d" xlink:type="arc" order="15"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1_019e6c04-3cf7-7618-8242-bdccbda8bea1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1_019e6c04-3cf7-7618-8242-bdccbda8bea1" xlink:type="arc" order="16"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_ClassOfWarrantOrRightFairValue_019e6c04-3cf7-7866-8c78-28e9caa08bca" xlink:href="cdxs-20260630.xsd#cdxs_ClassOfWarrantOrRightFairValue"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_DebtInstrumentLineItems_019e6c04-3cf7-73c6-8a1c-32230454c212" xlink:to="loc_cdxs_ClassOfWarrantOrRightFairValue_019e6c04-3cf7-7866-8c78-28e9caa08bca" xlink:type="arc" order="17"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/SegmentGeographicalandOtherRevenueInformationConcentrationRiskDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#SegmentGeographicalandOtherRevenueInformationConcentrationRiskDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/SegmentGeographicalandOtherRevenueInformationConcentrationRiskDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskLineItems_019e6c04-3cf7-7be0-8b6a-3f245334644a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskTable_019e6c04-3cf7-7e3a-9c56-77c8387f092c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_ConcentrationRiskLineItems_019e6c04-3cf7-7be0-8b6a-3f245334644a" xlink:to="loc_us-gaap_ConcentrationRiskTable_019e6c04-3cf7-7e3a-9c56-77c8387f092c" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskByTypeAxis_019e6c04-3cf7-7bac-ac9e-0364bb3554ea" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByTypeAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ConcentrationRiskTable_019e6c04-3cf7-7e3a-9c56-77c8387f092c" xlink:to="loc_us-gaap_ConcentrationRiskByTypeAxis_019e6c04-3cf7-7bac-ac9e-0364bb3554ea" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskTypeDomain_019e6c04-3cf7-7bac-ac9e-0364bb3554ea_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ConcentrationRiskByTypeAxis_019e6c04-3cf7-7bac-ac9e-0364bb3554ea" xlink:to="loc_us-gaap_ConcentrationRiskTypeDomain_019e6c04-3cf7-7bac-ac9e-0364bb3554ea_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskTypeDomain_019e6c04-3cf7-703c-b19a-e67c77df00ea" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ConcentrationRiskByTypeAxis_019e6c04-3cf7-7bac-ac9e-0364bb3554ea" xlink:to="loc_us-gaap_ConcentrationRiskTypeDomain_019e6c04-3cf7-703c-b19a-e67c77df00ea" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CustomerConcentrationRiskMember_019e6c04-3cf7-7d21-86f0-56f9dfef0ef1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CustomerConcentrationRiskMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskTypeDomain_019e6c04-3cf7-703c-b19a-e67c77df00ea" xlink:to="loc_us-gaap_CustomerConcentrationRiskMember_019e6c04-3cf7-7d21-86f0-56f9dfef0ef1" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_019e6c04-3cf7-77a4-a0ad-2b6dd26c46de" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskByBenchmarkAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ConcentrationRiskTable_019e6c04-3cf7-7e3a-9c56-77c8387f092c" xlink:to="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_019e6c04-3cf7-77a4-a0ad-2b6dd26c46de" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_019e6c04-3cf7-77a4-a0ad-2b6dd26c46de_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_019e6c04-3cf7-77a4-a0ad-2b6dd26c46de" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_019e6c04-3cf7-77a4-a0ad-2b6dd26c46de_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskBenchmarkDomain_019e6c04-3cf7-71b4-94bb-383ee8a6c080" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskBenchmarkDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_ConcentrationRiskByBenchmarkAxis_019e6c04-3cf7-77a4-a0ad-2b6dd26c46de" xlink:to="loc_us-gaap_ConcentrationRiskBenchmarkDomain_019e6c04-3cf7-71b4-94bb-383ee8a6c080" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SalesRevenueProductLineMember_019e6c04-3cf7-755e-9e17-af45e671b13d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SalesRevenueProductLineMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskBenchmarkDomain_019e6c04-3cf7-71b4-94bb-383ee8a6c080" xlink:to="loc_us-gaap_SalesRevenueProductLineMember_019e6c04-3cf7-755e-9e17-af45e671b13d" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccountsReceivableMember_019e6c04-3cf7-7a33-87d0-aff4ee6f3fb1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccountsReceivableMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskBenchmarkDomain_019e6c04-3cf7-71b4-94bb-383ee8a6c080" xlink:to="loc_us-gaap_AccountsReceivableMember_019e6c04-3cf7-7a33-87d0-aff4ee6f3fb1" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_MajorCustomersAxis_019e6c04-3cf7-7af1-a035-d05fe6a8a1bc" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_MajorCustomersAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ConcentrationRiskTable_019e6c04-3cf7-7e3a-9c56-77c8387f092c" xlink:to="loc_srt_MajorCustomersAxis_019e6c04-3cf7-7af1-a035-d05fe6a8a1bc" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7af1-a035-d05fe6a8a1bc_default" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_NameOfMajorCustomerDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_srt_MajorCustomersAxis_019e6c04-3cf7-7af1-a035-d05fe6a8a1bc" xlink:to="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7af1-a035-d05fe6a8a1bc_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:href="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd#srt_NameOfMajorCustomerDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_srt_MajorCustomersAxis_019e6c04-3cf7-7af1-a035-d05fe6a8a1bc" xlink:to="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerAMember_019e6c04-3cf7-7e95-ba5b-93855e47e648" xlink:href="cdxs-20260630.xsd#cdxs_CustomerAMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:to="loc_cdxs_CustomerAMember_019e6c04-3cf7-7e95-ba5b-93855e47e648" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerBMember_019e6c04-3cf7-7c0d-ac2d-32a34813e57f" xlink:href="cdxs-20260630.xsd#cdxs_CustomerBMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:to="loc_cdxs_CustomerBMember_019e6c04-3cf7-7c0d-ac2d-32a34813e57f" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerCMember_019e6c04-3cf7-7b68-96c0-f087c684d840" xlink:href="cdxs-20260630.xsd#cdxs_CustomerCMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:to="loc_cdxs_CustomerCMember_019e6c04-3cf7-7b68-96c0-f087c684d840" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerFMember_019e6c04-3cf7-774f-8884-6cd62699175c" xlink:href="cdxs-20260630.xsd#cdxs_CustomerFMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:to="loc_cdxs_CustomerFMember_019e6c04-3cf7-774f-8884-6cd62699175c" xlink:type="arc" order="3"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerGMember_019e6c04-3cf7-7236-a0f9-0b764221fc20" xlink:href="cdxs-20260630.xsd#cdxs_CustomerGMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:to="loc_cdxs_CustomerGMember_019e6c04-3cf7-7236-a0f9-0b764221fc20" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerHMember_019f846b-6ce7-7ee8-83ee-ac72b5b5b4b5" xlink:href="cdxs-20260630.xsd#cdxs_CustomerHMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:to="loc_cdxs_CustomerHMember_019f846b-6ce7-7ee8-83ee-ac72b5b5b4b5" xlink:type="arc" order="5"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerIMember_019f846c-1230-72bb-99cf-91b7237d39a3" xlink:href="cdxs-20260630.xsd#cdxs_CustomerIMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:to="loc_cdxs_CustomerIMember_019f846c-1230-72bb-99cf-91b7237d39a3" xlink:type="arc" order="6"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerDMember_019e6c04-3cf7-77a3-acd1-4655b09d8894" xlink:href="cdxs-20260630.xsd#cdxs_CustomerDMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:to="loc_cdxs_CustomerDMember_019e6c04-3cf7-77a3-acd1-4655b09d8894" xlink:type="arc" order="7"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerEMember_019e6c04-3cf7-7e68-af8e-103e49d533f5" xlink:href="cdxs-20260630.xsd#cdxs_CustomerEMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:to="loc_cdxs_CustomerEMember_019e6c04-3cf7-7e68-af8e-103e49d533f5" xlink:type="arc" order="8"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerJMember_019f8466-ab0a-7d32-90dc-a3d7c7edb51a" xlink:href="cdxs-20260630.xsd#cdxs_CustomerJMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:to="loc_cdxs_CustomerJMember_019f8466-ab0a-7d32-90dc-a3d7c7edb51a" xlink:type="arc" order="9"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_CustomerKMember_019f8465-d1d1-79d7-8a51-8887ad17a08a" xlink:href="cdxs-20260630.xsd#cdxs_CustomerKMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_srt_NameOfMajorCustomerDomain_019e6c04-3cf7-7185-8890-80fcf319405d" xlink:to="loc_cdxs_CustomerKMember_019f8465-d1d1-79d7-8a51-8887ad17a08a" xlink:type="arc" order="10"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ConcentrationRiskPercentage1_019e6c04-3cf7-708b-b9c9-a91e81618352" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ConcentrationRiskPercentage1"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_ConcentrationRiskLineItems_019e6c04-3cf7-7be0-8b6a-3f245334644a" xlink:to="loc_us-gaap_ConcentrationRiskPercentage1_019e6c04-3cf7-708b-b9c9-a91e81618352" xlink:type="arc" order="0"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/SegmentGeographicalandOtherRevenueInformationLongLivedAssetsbyGeographicAreaDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#SegmentGeographicalandOtherRevenueInformationLongLivedAssetsbyGeographicAreaDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/SegmentGeographicalandOtherRevenueInformationLongLivedAssetsbyGeographicAreaDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SegmentReportingInformationLineItems_019e6c04-3cf7-7791-a839-5c79daa27dbc" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SegmentReportingInformationLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ScheduleOfRevenuesFromExternalCustomersAndLongLivedAssetsTable_019e6c04-3cf7-71a1-a90a-ff29609eada3" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ScheduleOfRevenuesFromExternalCustomersAndLongLivedAssetsTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_SegmentReportingInformationLineItems_019e6c04-3cf7-7791-a839-5c79daa27dbc" xlink:to="loc_us-gaap_ScheduleOfRevenuesFromExternalCustomersAndLongLivedAssetsTable_019e6c04-3cf7-71a1-a90a-ff29609eada3" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_GeographicDistributionAxis_019e6c04-3cf7-79a5-bbd9-816c3158a609" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GeographicDistributionAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_ScheduleOfRevenuesFromExternalCustomersAndLongLivedAssetsTable_019e6c04-3cf7-71a1-a90a-ff29609eada3" xlink:to="loc_us-gaap_GeographicDistributionAxis_019e6c04-3cf7-79a5-bbd9-816c3158a609" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_GeographicDistributionDomain_019e6c04-3cf7-79a5-bbd9-816c3158a609_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GeographicDistributionDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_GeographicDistributionAxis_019e6c04-3cf7-79a5-bbd9-816c3158a609" xlink:to="loc_us-gaap_GeographicDistributionDomain_019e6c04-3cf7-79a5-bbd9-816c3158a609_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_GeographicDistributionDomain_019e6c04-3cf7-7eff-8361-2dada67f626c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GeographicDistributionDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_GeographicDistributionAxis_019e6c04-3cf7-79a5-bbd9-816c3158a609" xlink:to="loc_us-gaap_GeographicDistributionDomain_019e6c04-3cf7-7eff-8361-2dada67f626c" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_country_US_019e6c04-3cf7-7190-b9f9-446bebe07873" xlink:href="https://xbrl.sec.gov/country/2026/country-2026.xsd#country_US"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_GeographicDistributionDomain_019e6c04-3cf7-7eff-8361-2dada67f626c" xlink:to="loc_country_US_019e6c04-3cf7-7190-b9f9-446bebe07873" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_GeographicAreasLongLivedAssetsAbstract_019e6c04-3cf7-7429-b8b6-55c84470365b" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GeographicAreasLongLivedAssetsAbstract"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SegmentReportingInformationLineItems_019e6c04-3cf7-7791-a839-5c79daa27dbc" xlink:to="loc_us-gaap_GeographicAreasLongLivedAssetsAbstract_019e6c04-3cf7-7429-b8b6-55c84470365b" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NoncurrentAssets_019e6c04-3cf7-79b9-be90-56d777954c04" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NoncurrentAssets"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_GeographicAreasLongLivedAssetsAbstract_019e6c04-3cf7-7429-b8b6-55c84470365b" xlink:to="loc_us-gaap_NoncurrentAssets_019e6c04-3cf7-79b9-be90-56d777954c04" xlink:type="arc" order="1"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://www.codexis.com/role/SubsequentEventDetails" xlink:type="simple" xlink:href="cdxs-20260630.xsd#SubsequentEventDetails"/>
  <link:definitionLink xlink:role="http://www.codexis.com/role/SubsequentEventDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventLineItems_019e6c04-3cf7-75b4-80a3-13c59cdd74dd" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventLineItems"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTable_019e6c04-3cf7-75db-8167-2df290ebc657" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventTable"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="loc_us-gaap_SubsequentEventLineItems_019e6c04-3cf7-75b4-80a3-13c59cdd74dd" xlink:to="loc_us-gaap_SubsequentEventTable_019e6c04-3cf7-75db-8167-2df290ebc657" xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsidiarySaleOfStockAxis_019fa678-fe85-7fea-a65a-53a67342bf61" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsidiarySaleOfStockAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_SubsequentEventTable_019e6c04-3cf7-75db-8167-2df290ebc657" xlink:to="loc_us-gaap_SubsidiarySaleOfStockAxis_019fa678-fe85-7fea-a65a-53a67342bf61" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SaleOfStockNameOfTransactionDomain_019fa678-fe85-7fea-a65a-53a67342bf61_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_SubsidiarySaleOfStockAxis_019fa678-fe85-7fea-a65a-53a67342bf61" xlink:to="loc_us-gaap_SaleOfStockNameOfTransactionDomain_019fa678-fe85-7fea-a65a-53a67342bf61_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SaleOfStockNameOfTransactionDomain_019fa678-fe85-7d46-aaa1-4e6fd05e1bee" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_SubsidiarySaleOfStockAxis_019fa678-fe85-7fea-a65a-53a67342bf61" xlink:to="loc_us-gaap_SaleOfStockNameOfTransactionDomain_019fa678-fe85-7d46-aaa1-4e6fd05e1bee" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_PublicStockOfferingMember_019fa679-5a7a-7b25-b09f-0febd861517b" xlink:href="cdxs-20260630.xsd#cdxs_PublicStockOfferingMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SaleOfStockNameOfTransactionDomain_019fa678-fe85-7d46-aaa1-4e6fd05e1bee" xlink:to="loc_cdxs_PublicStockOfferingMember_019fa679-5a7a-7b25-b09f-0febd861517b" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OverAllotmentOptionMember_019fa680-6651-73b9-955e-286b07cf34af" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OverAllotmentOptionMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SaleOfStockNameOfTransactionDomain_019fa678-fe85-7d46-aaa1-4e6fd05e1bee" xlink:to="loc_us-gaap_OverAllotmentOptionMember_019fa680-6651-73b9-955e-286b07cf34af" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeAxis_019fa682-505f-7ea6-974c-0fac2c2ba216" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventTypeAxis"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="loc_us-gaap_SubsequentEventTable_019e6c04-3cf7-75db-8167-2df290ebc657" xlink:to="loc_us-gaap_SubsequentEventTypeAxis_019fa682-505f-7ea6-974c-0fac2c2ba216" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeDomain_019fa682-505f-7ea6-974c-0fac2c2ba216_default" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="loc_us-gaap_SubsequentEventTypeAxis_019fa682-505f-7ea6-974c-0fac2c2ba216" xlink:to="loc_us-gaap_SubsequentEventTypeDomain_019fa682-505f-7ea6-974c-0fac2c2ba216_default" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventTypeDomain_019fa682-505f-70d3-9182-ed0d036dd2b1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventTypeDomain"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="loc_us-gaap_SubsequentEventTypeAxis_019fa682-505f-7ea6-974c-0fac2c2ba216" xlink:to="loc_us-gaap_SubsequentEventTypeDomain_019fa682-505f-70d3-9182-ed0d036dd2b1" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SubsequentEventMember_019fa682-6a51-7fae-a9d7-cec916eeb600" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SubsequentEventMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventTypeDomain_019fa682-505f-70d3-9182-ed0d036dd2b1" xlink:to="loc_us-gaap_SubsequentEventMember_019fa682-6a51-7fae-a9d7-cec916eeb600" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SaleOfStockNumberOfSharesIssuedInTransaction_019fa683-79fe-771b-8a4c-8dcd3e8bb647" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SaleOfStockNumberOfSharesIssuedInTransaction"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventLineItems_019e6c04-3cf7-75b4-80a3-13c59cdd74dd" xlink:to="loc_us-gaap_SaleOfStockNumberOfSharesIssuedInTransaction_019fa683-79fe-771b-8a4c-8dcd3e8bb647" xlink:type="arc" order="0"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SaleOfStockPricePerShare_019fa683-79fe-7854-98fd-47036dd0c060" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SaleOfStockPricePerShare"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventLineItems_019e6c04-3cf7-75b4-80a3-13c59cdd74dd" xlink:to="loc_us-gaap_SaleOfStockPricePerShare_019fa683-79fe-7854-98fd-47036dd0c060" xlink:type="arc" order="1"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_SaleOfStockOfferingOptionTerm_019fa683-79fe-7f49-adcd-3a98f72206dc" xlink:href="cdxs-20260630.xsd#cdxs_SaleOfStockOfferingOptionTerm"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventLineItems_019e6c04-3cf7-75b4-80a3-13c59cdd74dd" xlink:to="loc_cdxs_SaleOfStockOfferingOptionTerm_019fa683-79fe-7f49-adcd-3a98f72206dc" xlink:type="arc" order="2"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_SaleOfStockConsiderationReceivedOnTransaction_019fa683-79fe-727c-9e87-663956fcc5cc" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SaleOfStockConsiderationReceivedOnTransaction"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_us-gaap_SubsequentEventLineItems_019e6c04-3cf7-75b4-80a3-13c59cdd74dd" xlink:to="loc_us-gaap_SaleOfStockConsiderationReceivedOnTransaction_019fa683-79fe-727c-9e87-663956fcc5cc" xlink:type="arc" order="3"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://xbrl.sec.gov/ecd/role/IndividualsOnly" xlink:type="simple" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#IndividualsOnly"/>
  <link:definitionLink xlink:role="http://xbrl.sec.gov/ecd/role/IndividualsOnly" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_ecd_AllIndividualsMember" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_AllIndividualsMember"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_StefanLutzMember_019fbfa2-533c-73df-9c11-0d3df40ef6a2" xlink:href="cdxs-20260630.xsd#cdxs_StefanLutzMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_ecd_AllIndividualsMember" xlink:to="loc_cdxs_StefanLutzMember_019fbfa2-533c-73df-9c11-0d3df40ef6a2" xlink:type="arc" order="2"/>
  </link:definitionLink>
  <link:roleRef roleURI="http://xbrl.sec.gov/ecd/role/TradingArrangementsOnly" xlink:type="simple" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#TradingArrangmentsOnly"/>
  <link:definitionLink xlink:role="http://xbrl.sec.gov/ecd/role/TradingArrangementsOnly" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_ecd_AllTradingArrangementsMember" xlink:href="https://xbrl.sec.gov/ecd/2026/ecd-2026.xsd#ecd_AllTradingArrangementsMember"/>
    <link:loc xlink:type="locator" xlink:label="loc_cdxs_StefanLutzSeptember2025PlanMember_019fbfae-8d63-7e8a-ad0b-df3049b850ed" xlink:href="cdxs-20260630.xsd#cdxs_StefanLutzSeptember2025PlanMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_ecd_AllTradingArrangementsMember" xlink:to="loc_cdxs_StefanLutzSeptember2025PlanMember_019fbfae-8d63-7e8a-ad0b-df3049b850ed" xlink:type="arc" order="1"/>
  </link:definitionLink>
</link:linkbase>
