<?xml version="1.0" encoding="US-ASCII" standalone="no"?>
<!--Generated by ThunderDome XBRL - 07:25PM UTC 2026-08-04--><link:linkbase xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:roleRef roleURI="http://www.naturalgrocers.com/20260630/role/statement-consolidated-balance-sheets-current-period-unaudited" xlink:href="ngvc-20260630.xsd#statement-consolidated-balance-sheets-current-period-unaudited" xlink:type="simple"/>
  <link:calculationLink xlink:role="http://www.naturalgrocers.com/20260630/role/statement-consolidated-balance-sheets-current-period-unaudited" xlink:type="extended">
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_AssetsNoncurrentExcludingPropertyPlantAndEquipment" xlink:label="ngvc_AssetsNoncurrentExcludingPropertyPlantAndEquipment" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccountsPayableCurrent" xlink:label="us-gaap_AccountsPayableCurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccountsReceivableNetCurrent" xlink:label="us-gaap_AccountsReceivableNetCurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:label="us-gaap_AccruedLiabilitiesCurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AdditionalPaidInCapitalCommonStock" xlink:label="us-gaap_AdditionalPaidInCapitalCommonStock" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Assets" xlink:label="us-gaap_Assets" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AssetsCurrent" xlink:label="us-gaap_AssetsCurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommonStockValue" xlink:label="us-gaap_CommonStockValue" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DeferredIncomeTaxLiabilitiesNet" xlink:label="us-gaap_DeferredIncomeTaxLiabilitiesNet" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinanceLeaseLiabilityCurrent" xlink:label="us-gaap_FinanceLeaseLiabilityCurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinanceLeaseLiabilityNoncurrent" xlink:label="us-gaap_FinanceLeaseLiabilityNoncurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinanceLeaseRightOfUseAsset" xlink:label="us-gaap_FinanceLeaseRightOfUseAsset" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IntangibleAssetsNetIncludingGoodwill" xlink:label="us-gaap_IntangibleAssetsNetIncludingGoodwill" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Liabilities" xlink:label="us-gaap_Liabilities" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LiabilitiesAndStockholdersEquity" xlink:label="us-gaap_LiabilitiesAndStockholdersEquity" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LiabilitiesCurrent" xlink:label="us-gaap_LiabilitiesCurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LiabilitiesNoncurrent" xlink:label="us-gaap_LiabilitiesNoncurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LongTermDebtCurrent" xlink:label="us-gaap_LongTermDebtCurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LongTermDebtNoncurrent" xlink:label="us-gaap_LongTermDebtNoncurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseLiabilityCurrent" xlink:label="us-gaap_OperatingLeaseLiabilityCurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:label="us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseRightOfUseAsset" xlink:label="us-gaap_OperatingLeaseRightOfUseAsset" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherAssetsNoncurrent" xlink:label="us-gaap_OtherAssetsNoncurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:label="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:label="us-gaap_PropertyPlantAndEquipmentNet" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RetailRelatedInventoryMerchandise" xlink:label="us-gaap_RetailRelatedInventoryMerchandise" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockholdersEquity" xlink:label="us-gaap_StockholdersEquity" xlink:type="locator"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_AccountsReceivableNetCurrent" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_RetailRelatedInventoryMerchandise" xlink:type="arc"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="ngvc_AssetsNoncurrentExcludingPropertyPlantAndEquipment" xlink:to="us-gaap_FinanceLeaseRightOfUseAsset" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="ngvc_AssetsNoncurrentExcludingPropertyPlantAndEquipment" xlink:to="us-gaap_OtherAssetsNoncurrent" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="ngvc_AssetsNoncurrentExcludingPropertyPlantAndEquipment" xlink:to="us-gaap_IntangibleAssetsNetIncludingGoodwill" xlink:type="arc"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="ngvc_AssetsNoncurrentExcludingPropertyPlantAndEquipment" xlink:to="us-gaap_OperatingLeaseRightOfUseAsset" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="ngvc_AssetsNoncurrentExcludingPropertyPlantAndEquipment" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_AssetsCurrent" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_PropertyPlantAndEquipmentNet" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_LongTermDebtCurrent" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_OperatingLeaseLiabilityCurrent" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_FinanceLeaseLiabilityCurrent" xlink:type="arc"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_AccountsPayableCurrent" xlink:type="arc"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_AccruedLiabilitiesCurrent" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesNoncurrent" xlink:to="us-gaap_LongTermDebtNoncurrent" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesNoncurrent" xlink:to="us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesNoncurrent" xlink:to="us-gaap_FinanceLeaseLiabilityNoncurrent" xlink:type="arc"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesNoncurrent" xlink:to="us-gaap_DeferredIncomeTaxLiabilitiesNet" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_LiabilitiesNoncurrent" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_LiabilitiesCurrent" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_AdditionalPaidInCapitalCommonStock" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_CommonStockValue" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_Liabilities" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_StockholdersEquity" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.naturalgrocers.com/20260630/role/statement-consolidated-statements-of-income-unaudited" xlink:href="ngvc-20260630.xsd#statement-consolidated-statements-of-income-unaudited" xlink:type="simple"/>
  <link:calculationLink xlink:role="http://www.naturalgrocers.com/20260630/role/statement-consolidated-statements-of-income-unaudited" xlink:type="extended">
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_CostOfGoodsSoldAndOccupancyCosts" xlink:label="ngvc_CostOfGoodsSoldAndOccupancyCosts" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_PreOpeningCostsAndRelocationExpenses" xlink:label="ngvc_PreOpeningCostsAndRelocationExpenses" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_StoreExpenses" xlink:label="ngvc_StoreExpenses" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GeneralAndAdministrativeExpense" xlink:label="us-gaap_GeneralAndAdministrativeExpense" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GrossProfit" xlink:label="us-gaap_GrossProfit" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest" xlink:label="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncomeTaxExpenseBenefit" xlink:label="us-gaap_IncomeTaxExpenseBenefit" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InterestExpense" xlink:label="us-gaap_InterestExpense" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingIncomeLoss" xlink:label="us-gaap_OperatingIncomeLoss" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:type="locator"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_GrossProfit" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:type="arc"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_GrossProfit" xlink:to="ngvc_CostOfGoodsSoldAndOccupancyCosts" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="us-gaap_GrossProfit" xlink:type="arc"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="ngvc_StoreExpenses" xlink:type="arc"/>
    <link:calculationArc order="2" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="us-gaap_GeneralAndAdministrativeExpense" xlink:type="arc"/>
    <link:calculationArc order="3" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="ngvc_PreOpeningCostsAndRelocationExpenses" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest" xlink:to="us-gaap_OperatingIncomeLoss" xlink:type="arc"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest" xlink:to="us-gaap_InterestExpense" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest" xlink:type="arc"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_IncomeTaxExpenseBenefit" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.naturalgrocers.com/20260630/role/statement-consolidated-statements-of-cash-flows-unaudited" xlink:href="ngvc-20260630.xsd#statement-consolidated-statements-of-cash-flows-unaudited" xlink:type="simple"/>
  <link:calculationLink xlink:role="http://www.naturalgrocers.com/20260630/role/statement-consolidated-statements-of-cash-flows-unaudited" xlink:type="extended">
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_ImpairmentOfLonglivedAssetsAndStoreClosingCosts" xlink:label="ngvc_ImpairmentOfLonglivedAssetsAndStoreClosingCosts" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_IncreaseDecreaseInOperatingLeaseAsset" xlink:label="ngvc_IncreaseDecreaseInOperatingLeaseAsset" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AmortizationOfFinancingCosts" xlink:label="us-gaap_AmortizationOfFinancingCosts" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DeferredIncomeTaxExpenseBenefit" xlink:label="us-gaap_DeferredIncomeTaxExpenseBenefit" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DepreciationDepletionAndAmortization" xlink:label="us-gaap_DepreciationDepletionAndAmortization" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinanceLeasePrincipalPayments" xlink:label="us-gaap_FinanceLeasePrincipalPayments" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GainLossOnSaleOfPropertyPlantEquipment" xlink:label="us-gaap_GainLossOnSaleOfPropertyPlantEquipment" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInAccountsPayableTrade" xlink:label="us-gaap_IncreaseDecreaseInAccountsPayableTrade" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInAccountsReceivable" xlink:label="us-gaap_IncreaseDecreaseInAccountsReceivable" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInAccruedLiabilities" xlink:label="us-gaap_IncreaseDecreaseInAccruedLiabilities" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInIncomeTaxesReceivable" xlink:label="us-gaap_IncreaseDecreaseInIncomeTaxesReceivable" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInInventories" xlink:label="us-gaap_IncreaseDecreaseInInventories" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInOperatingLeaseLiability" xlink:label="us-gaap_IncreaseDecreaseInOperatingLeaseLiability" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:label="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherNoncashIncomeExpense" xlink:label="us-gaap_OtherNoncashIncomeExpense" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PaymentsOfDividendsCommonStock" xlink:label="us-gaap_PaymentsOfDividendsCommonStock" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PaymentsRelatedToTaxWithholdingForShareBasedCompensation" xlink:label="us-gaap_PaymentsRelatedToTaxWithholdingForShareBasedCompensation" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PaymentsToAcquireIntangibleAssets" xlink:label="us-gaap_PaymentsToAcquireIntangibleAssets" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:label="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ProceedsFromInsuranceSettlementInvestingActivities" xlink:label="us-gaap_ProceedsFromInsuranceSettlementInvestingActivities" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ProceedsFromLinesOfCredit" xlink:label="us-gaap_ProceedsFromLinesOfCredit" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment" xlink:label="us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RepaymentsOfLinesOfCredit" xlink:label="us-gaap_RepaymentsOfLinesOfCredit" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensation" xlink:label="us-gaap_ShareBasedCompensation" xlink:type="locator"/>
    <link:calculationArc order="0" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInInventories" xlink:type="arc"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:type="arc"/>
    <link:calculationArc order="2" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInIncomeTaxesReceivable" xlink:type="arc"/>
    <link:calculationArc order="3" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="ngvc_IncreaseDecreaseInOperatingLeaseAsset" xlink:type="arc"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInOperatingLeaseLiability" xlink:type="arc"/>
    <link:calculationArc order="5" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInAccountsPayableTrade" xlink:type="arc"/>
    <link:calculationArc order="6" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_NetIncomeLoss" xlink:type="arc"/>
    <link:calculationArc order="7" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInAccruedLiabilities" xlink:type="arc"/>
    <link:calculationArc order="8" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_DepreciationDepletionAndAmortization" xlink:type="arc"/>
    <link:calculationArc order="9" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="ngvc_ImpairmentOfLonglivedAssetsAndStoreClosingCosts" xlink:type="arc"/>
    <link:calculationArc order="10" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_GainLossOnSaleOfPropertyPlantEquipment" xlink:type="arc"/>
    <link:calculationArc order="11" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_ShareBasedCompensation" xlink:type="arc"/>
    <link:calculationArc order="12" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_DeferredIncomeTaxExpenseBenefit" xlink:type="arc"/>
    <link:calculationArc order="13" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_AmortizationOfFinancingCosts" xlink:type="arc"/>
    <link:calculationArc order="14" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_OtherNoncashIncomeExpense" xlink:type="arc"/>
    <link:calculationArc order="15" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInAccountsReceivable" xlink:type="arc"/>
    <link:calculationArc order="0" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:type="arc"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_PaymentsToAcquireIntangibleAssets" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_ProceedsFromSaleOfPropertyPlantAndEquipment" xlink:type="arc"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_ProceedsFromInsuranceSettlementInvestingActivities" xlink:type="arc"/>
    <link:calculationArc order="0" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_FinanceLeasePrincipalPayments" xlink:type="arc"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_PaymentsOfDividendsCommonStock" xlink:type="arc"/>
    <link:calculationArc order="2" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_PaymentsRelatedToTaxWithholdingForShareBasedCompensation" xlink:type="arc"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_ProceedsFromLinesOfCredit" xlink:type="arc"/>
    <link:calculationArc order="4" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_RepaymentsOfLinesOfCredit" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.naturalgrocers.com/20260630/role/statement-note-4-earnings-per-share-basic-and-diluted-earnings-per-share-details" xlink:href="ngvc-20260630.xsd#statement-note-4-earnings-per-share-basic-and-diluted-earnings-per-share-details" xlink:type="simple"/>
  <link:calculationLink xlink:role="http://www.naturalgrocers.com/20260630/role/statement-note-4-earnings-per-share-basic-and-diluted-earnings-per-share-details" xlink:type="extended">
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustment" xlink:label="us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustment" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" xlink:label="us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_WeightedAverageNumberOfSharesOutstandingBasic" xlink:label="us-gaap_WeightedAverageNumberOfSharesOutstandingBasic" xlink:type="locator"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" xlink:to="us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustment" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" xlink:to="us-gaap_WeightedAverageNumberOfSharesOutstandingBasic" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.naturalgrocers.com/20260630/role/statement-note-7-leases-future-lease-payments-details" xlink:href="ngvc-20260630.xsd#statement-note-7-leases-future-lease-payments-details" xlink:type="simple"/>
  <link:calculationLink xlink:role="http://www.naturalgrocers.com/20260630/role/statement-note-7-leases-future-lease-payments-details" xlink:type="extended">
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_FinanceLeaseLiabilityToBePaidAfterYearFour" xlink:label="ngvc_FinanceLeaseLiabilityToBePaidAfterYearFour" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDue" xlink:label="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDue" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueAfterYearFour" xlink:label="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueAfterYearFour" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueYearFour" xlink:label="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueYearFour" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueYearOne" xlink:label="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueYearOne" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueYearThree" xlink:label="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueYearThree" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueYearTwo" xlink:label="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueYearTwo" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsRemainderOfFiscalYear" xlink:label="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsRemainderOfFiscalYear" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_LesseeOperatingLeaseLiabilityToBePaidAfterYearFour" xlink:label="ngvc_LesseeOperatingLeaseLiabilityToBePaidAfterYearFour" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinanceLeaseLiabilityPaymentsDue" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsDue" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinanceLeaseLiabilityPaymentsDueNextTwelveMonths" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsDueNextTwelveMonths" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinanceLeaseLiabilityPaymentsDueYearFour" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsDueYearFour" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinanceLeaseLiabilityPaymentsDueYearThree" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsDueYearThree" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinanceLeaseLiabilityPaymentsDueYearTwo" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsDueYearTwo" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FinanceLeaseLiabilityPaymentsRemainderOfFiscalYear" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsRemainderOfFiscalYear" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsRemainderOfFiscalYear" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsRemainderOfFiscalYear" xlink:type="locator"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree" xlink:type="arc"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour" xlink:type="arc"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="ngvc_LesseeOperatingLeaseLiabilityToBePaidAfterYearFour" xlink:type="arc"/>
    <link:calculationArc order="5" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsRemainderOfFiscalYear" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_FinanceLeaseLiabilityPaymentsDue" xlink:to="us-gaap_FinanceLeaseLiabilityPaymentsRemainderOfFiscalYear" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_FinanceLeaseLiabilityPaymentsDue" xlink:to="us-gaap_FinanceLeaseLiabilityPaymentsDueNextTwelveMonths" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_FinanceLeaseLiabilityPaymentsDue" xlink:to="us-gaap_FinanceLeaseLiabilityPaymentsDueYearTwo" xlink:type="arc"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_FinanceLeaseLiabilityPaymentsDue" xlink:to="us-gaap_FinanceLeaseLiabilityPaymentsDueYearThree" xlink:type="arc"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_FinanceLeaseLiabilityPaymentsDue" xlink:to="us-gaap_FinanceLeaseLiabilityPaymentsDueYearFour" xlink:type="arc"/>
    <link:calculationArc order="5" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_FinanceLeaseLiabilityPaymentsDue" xlink:to="ngvc_FinanceLeaseLiabilityToBePaidAfterYearFour" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDue" xlink:to="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueAfterYearFour" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDue" xlink:to="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsRemainderOfFiscalYear" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDue" xlink:to="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueYearOne" xlink:type="arc"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDue" xlink:to="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueYearTwo" xlink:type="arc"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDue" xlink:to="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueYearThree" xlink:type="arc"/>
    <link:calculationArc order="5" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDue" xlink:to="ngvc_LesseeOperatingAndFinanceLeaseLiabilityPaymentsDueYearFour" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.naturalgrocers.com/20260630/role/statement-note-7-leases-lease-income-details" xlink:href="ngvc-20260630.xsd#statement-note-7-leases-lease-income-details" xlink:type="simple"/>
  <link:calculationLink xlink:role="http://www.naturalgrocers.com/20260630/role/statement-note-7-leases-lease-income-details" xlink:type="extended">
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseLeaseIncome" xlink:label="us-gaap_OperatingLeaseLeaseIncome" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseLeaseIncomeLeasePayments" xlink:label="us-gaap_OperatingLeaseLeaseIncomeLeasePayments" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseVariableLeaseIncome" xlink:label="us-gaap_OperatingLeaseVariableLeaseIncome" xlink:type="locator"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeaseLeaseIncome" xlink:to="us-gaap_OperatingLeaseLeaseIncomeLeasePayments" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeaseLeaseIncome" xlink:to="us-gaap_OperatingLeaseVariableLeaseIncome" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.naturalgrocers.com/20260630/role/statement-note-7-leases-future-undiscounted-lease-collections-details" xlink:href="ngvc-20260630.xsd#statement-note-7-leases-future-undiscounted-lease-collections-details" xlink:type="simple"/>
  <link:calculationLink xlink:role="http://www.naturalgrocers.com/20260630/role/statement-note-7-leases-future-undiscounted-lease-collections-details" xlink:type="extended">
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_LessorOperatingLeasePaymentToBeReceivedAfterYearFive" xlink:label="ngvc_LessorOperatingLeasePaymentToBeReceivedAfterYearFive" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LessorOperatingLeasePaymentsToBeReceived" xlink:label="us-gaap_LessorOperatingLeasePaymentsToBeReceived" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LessorOperatingLeasePaymentsToBeReceivedFourYears" xlink:label="us-gaap_LessorOperatingLeasePaymentsToBeReceivedFourYears" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LessorOperatingLeasePaymentsToBeReceivedNextTwelveMonths" xlink:label="us-gaap_LessorOperatingLeasePaymentsToBeReceivedNextTwelveMonths" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LessorOperatingLeasePaymentsToBeReceivedRemainderOfFiscalYear" xlink:label="us-gaap_LessorOperatingLeasePaymentsToBeReceivedRemainderOfFiscalYear" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LessorOperatingLeasePaymentsToBeReceivedThreeYears" xlink:label="us-gaap_LessorOperatingLeasePaymentsToBeReceivedThreeYears" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LessorOperatingLeasePaymentsToBeReceivedTwoYears" xlink:label="us-gaap_LessorOperatingLeasePaymentsToBeReceivedTwoYears" xlink:type="locator"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LessorOperatingLeasePaymentsToBeReceived" xlink:to="us-gaap_LessorOperatingLeasePaymentsToBeReceivedRemainderOfFiscalYear" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LessorOperatingLeasePaymentsToBeReceived" xlink:to="us-gaap_LessorOperatingLeasePaymentsToBeReceivedNextTwelveMonths" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LessorOperatingLeasePaymentsToBeReceived" xlink:to="us-gaap_LessorOperatingLeasePaymentsToBeReceivedTwoYears" xlink:type="arc"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LessorOperatingLeasePaymentsToBeReceived" xlink:to="us-gaap_LessorOperatingLeasePaymentsToBeReceivedThreeYears" xlink:type="arc"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LessorOperatingLeasePaymentsToBeReceived" xlink:to="us-gaap_LessorOperatingLeasePaymentsToBeReceivedFourYears" xlink:type="arc"/>
    <link:calculationArc order="5" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LessorOperatingLeasePaymentsToBeReceived" xlink:to="ngvc_LessorOperatingLeasePaymentToBeReceivedAfterYearFive" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.naturalgrocers.com/20260630/role/statement-note-8-property-and-equipment-schedule-of-property-and-equipment-details" xlink:href="ngvc-20260630.xsd#statement-note-8-property-and-equipment-schedule-of-property-and-equipment-details" xlink:type="simple"/>
  <link:calculationLink xlink:role="http://www.naturalgrocers.com/20260630/role/statement-note-8-property-and-equipment-schedule-of-property-and-equipment-details" xlink:type="extended">
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentExcludingLessorAssetUnderOperatingLeaseAccumulatedDepreciation" xlink:label="us-gaap_PropertyPlantAndEquipmentExcludingLessorAssetUnderOperatingLeaseAccumulatedDepreciation" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentExcludingLessorAssetUnderOperatingLeaseAfterAccumulatedDepreciation" xlink:label="us-gaap_PropertyPlantAndEquipmentExcludingLessorAssetUnderOperatingLeaseAfterAccumulatedDepreciation" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentExcludingLessorAssetUnderOperatingLeaseBeforeAccumulatedDepreciation" xlink:label="us-gaap_PropertyPlantAndEquipmentExcludingLessorAssetUnderOperatingLeaseBeforeAccumulatedDepreciation" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:label="us-gaap_PropertyPlantAndEquipmentNet" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertySubjectToOrAvailableForOperatingLeaseAccumulatedDepreciation" xlink:label="us-gaap_PropertySubjectToOrAvailableForOperatingLeaseAccumulatedDepreciation" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertySubjectToOrAvailableForOperatingLeaseGross" xlink:label="us-gaap_PropertySubjectToOrAvailableForOperatingLeaseGross" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertySubjectToOrAvailableForOperatingLeaseNet" xlink:label="us-gaap_PropertySubjectToOrAvailableForOperatingLeaseNet" xlink:type="locator"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_PropertyPlantAndEquipmentExcludingLessorAssetUnderOperatingLeaseAfterAccumulatedDepreciation" xlink:to="us-gaap_PropertyPlantAndEquipmentExcludingLessorAssetUnderOperatingLeaseBeforeAccumulatedDepreciation" xlink:type="arc"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_PropertyPlantAndEquipmentExcludingLessorAssetUnderOperatingLeaseAfterAccumulatedDepreciation" xlink:to="us-gaap_PropertyPlantAndEquipmentExcludingLessorAssetUnderOperatingLeaseAccumulatedDepreciation" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_PropertySubjectToOrAvailableForOperatingLeaseNet" xlink:to="us-gaap_PropertySubjectToOrAvailableForOperatingLeaseGross" xlink:type="arc"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_PropertySubjectToOrAvailableForOperatingLeaseNet" xlink:to="us-gaap_PropertySubjectToOrAvailableForOperatingLeaseAccumulatedDepreciation" xlink:type="arc"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_PropertyPlantAndEquipmentNet" xlink:to="us-gaap_PropertySubjectToOrAvailableForOperatingLeaseNet" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_PropertyPlantAndEquipmentNet" xlink:to="us-gaap_PropertyPlantAndEquipmentExcludingLessorAssetUnderOperatingLeaseAfterAccumulatedDepreciation" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.naturalgrocers.com/20260630/role/statement-note-10-goodwill-and-other-intangible-assets-summary-of-goodwill-and-other-intangible-assets-details" xlink:href="ngvc-20260630.xsd#statement-note-10-goodwill-and-other-intangible-assets-summary-of-goodwill-and-other-intangible-assets-details" xlink:type="simple"/>
  <link:calculationLink xlink:role="http://www.naturalgrocers.com/20260630/role/statement-note-10-goodwill-and-other-intangible-assets-summary-of-goodwill-and-other-intangible-assets-details" xlink:type="extended">
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_InternalUseSoftwareInProcess" xlink:label="ngvc_InternalUseSoftwareInProcess" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_FiniteLivedIntangibleAssetsNet" xlink:label="us-gaap_FiniteLivedIntangibleAssetsNet" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Goodwill" xlink:label="us-gaap_Goodwill" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IntangibleAssetsNetExcludingGoodwill" xlink:label="us-gaap_IntangibleAssetsNetExcludingGoodwill" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IntangibleAssetsNetIncludingGoodwill" xlink:label="us-gaap_IntangibleAssetsNetIncludingGoodwill" xlink:type="locator"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IntangibleAssetsNetIncludingGoodwill" xlink:to="us-gaap_IntangibleAssetsNetExcludingGoodwill" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IntangibleAssetsNetIncludingGoodwill" xlink:to="us-gaap_Goodwill" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IntangibleAssetsNetIncludingGoodwill" xlink:to="us-gaap_FiniteLivedIntangibleAssetsNet" xlink:type="arc"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IntangibleAssetsNetIncludingGoodwill" xlink:to="ngvc_InternalUseSoftwareInProcess" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.naturalgrocers.com/20260630/role/statement-note-11-accrued-expenses-composition-of-accrued-expenses-details" xlink:href="ngvc-20260630.xsd#statement-note-11-accrued-expenses-composition-of-accrued-expenses-details" xlink:type="simple"/>
  <link:calculationLink xlink:role="http://www.naturalgrocers.com/20260630/role/statement-note-11-accrued-expenses-composition-of-accrued-expenses-details" xlink:type="extended">
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_AccruedIncomePropertySalesAndUseTaxPayable" xlink:label="ngvc_AccruedIncomePropertySalesAndUseTaxPayable" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_DeferredRevenueGiftCards" xlink:label="ngvc_DeferredRevenueGiftCards" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:label="us-gaap_AccruedLiabilitiesCurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccruedMarketingCostsCurrent" xlink:label="us-gaap_AccruedMarketingCostsCurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeRelatedLiabilitiesCurrent" xlink:label="us-gaap_EmployeeRelatedLiabilitiesCurrent" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherAccruedLiabilitiesCurrent" xlink:label="us-gaap_OtherAccruedLiabilitiesCurrent" xlink:type="locator"/>
    <link:calculationArc order="0" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="us-gaap_OtherAccruedLiabilitiesCurrent" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="us-gaap_EmployeeRelatedLiabilitiesCurrent" xlink:type="arc"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="ngvc_AccruedIncomePropertySalesAndUseTaxPayable" xlink:type="arc"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="us-gaap_AccruedMarketingCostsCurrent" xlink:type="arc"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="ngvc_DeferredRevenueGiftCards" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.naturalgrocers.com/20260630/role/statement-note-14-segment-reporting-schedule-of-segment-reporting-information-details" xlink:href="ngvc-20260630.xsd#statement-note-14-segment-reporting-schedule-of-segment-reporting-information-details" xlink:type="simple"/>
  <link:calculationLink xlink:role="http://www.naturalgrocers.com/20260630/role/statement-note-14-segment-reporting-schedule-of-segment-reporting-information-details" xlink:type="extended">
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_CostOfGoodsSoldAndOccupancyCosts" xlink:label="ngvc_CostOfGoodsSoldAndOccupancyCosts" xlink:type="locator"/>
    <link:loc xlink:href="ngvc-20260630.xsd#ngvc_PreOpeningCostsAndRelocationExpenses" xlink:label="ngvc_PreOpeningCostsAndRelocationExpenses" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncomeTaxExpenseBenefit" xlink:label="us-gaap_IncomeTaxExpenseBenefit" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InterestExpense" xlink:label="us-gaap_InterestExpense" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingExpenses" xlink:label="us-gaap_OperatingExpenses" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:type="locator"/>
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_SegmentReportingOtherItemAmount" xlink:label="us-gaap_SegmentReportingOtherItemAmount" xlink:type="locator"/>
    <link:calculationArc order="0" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_SegmentReportingOtherItemAmount" xlink:type="arc"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:type="arc"/>
    <link:calculationArc order="2" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_InterestExpense" xlink:type="arc"/>
    <link:calculationArc order="3" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="ngvc_CostOfGoodsSoldAndOccupancyCosts" xlink:type="arc"/>
    <link:calculationArc order="4" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_IncomeTaxExpenseBenefit" xlink:type="arc"/>
    <link:calculationArc order="5" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_OperatingExpenses" xlink:type="arc"/>
    <link:calculationArc order="6" weight="-1.0" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="ngvc_PreOpeningCostsAndRelocationExpenses" xlink:type="arc"/>
  </link:calculationLink>
</link:linkbase>
