<?xml version="1.0" encoding="UTF-8" standalone="no"?><!--ICGIG V1.0 (06-10-2025)--><xbrli:xbrl xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:in-capmkt="http://www.sebi.gov.in/xbrl/2024-12-31/in-capmkt" xmlns:in-capmkt-ent="http://www.sebi.gov.in/xbrl/IntegratedGovernance/2024-12-31/in-capmkt/in-capmkt-ent" xmlns:in-capmkt-roles="http://www.sebi.gov.in/xbrl/IntegratedGovernance/2024-12-31/in-capmkt-roles" xmlns:in-capmkt-types="http://www.sebi.gov.in/xbrl/2024-12-31/in-capmkt-types" xmlns:iso4217="http://www.xbrl.org/2003/iso4217" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:negated="http://www.xbrl.org/2009/role/negated" xmlns:net="http://www.xbrl.org/2009/role/net" xmlns:nonnum="http://www.xbrl.org/dtr/type/non-numeric" xmlns:num="http://www.xbrl.org/dtr/type/numeric" xmlns:xbrldi="http://xbrl.org/2006/xbrldi" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:xl="http://www.xbrl.org/2003/XLink" xmlns:xlink="http://www.w3.org/1999/xlink"><link:schemaRef xlink:href="in-capmkt-ent-2024-12-31.xsd" xlink:type="simple"/><xbrli:context id="MainD"><xbrli:entity><xbrli:identifier scheme="https://www.sebi.gov.in/in-capmkt/Symbol">ARUNAYA</xbrli:identifier></xbrli:entity><xbrli:period><xbrli:startDate>2025-07-01</xbrli:startDate><xbrli:endDate>2025-09-30</xbrli:endDate></xbrli:period></xbrli:context><xbrli:context id="MainI"><xbrli:entity><xbrli:identifier scheme="https://www.sebi.gov.in/in-capmkt/Symbol">ARUNAYA</xbrli:identifier></xbrli:entity><xbrli:period><xbrli:instant>2025-09-30</xbrli:instant></xbrli:period></xbrli:context><xbrli:context id="PY_I"><xbrli:entity><xbrli:identifier scheme="https://www.sebi.gov.in/in-capmkt/Symbol">ARUNAYA</xbrli:identifier></xbrli:entity><xbrli:period><xbrli:instant>2025-06-30</xbrli:instant></xbrli:period></xbrli:context><xbrli:context id="I_ImpositionOfFineOrPenalty1"><xbrli:entity><xbrli:identifier scheme="https://www.sebi.gov.in/in-capmkt/Symbol">ARUNAYA</xbrli:identifier></xbrli:entity><xbrli:period><xbrli:instant>2025-09-30</xbrli:instant></xbrli:period><xbrli:scenario><xbrldi:typedMember dimension="in-capmkt:ImpositionOfFineOrPenaltyAxis"><in-capmkt:ImpositionOfFineOrPenaltyDomain>ImpositionOfFineOrPenaltyDomain1</in-capmkt:ImpositionOfFineOrPenaltyDomain></xbrldi:typedMember></xbrli:scenario></xbrli:context><xbrli:context id="I_OngoingTaxLitigationsOrDisputes1"><xbrli:entity><xbrli:identifier scheme="https://www.sebi.gov.in/in-capmkt/Symbol">ARUNAYA</xbrli:identifier></xbrli:entity><xbrli:period><xbrli:instant>2025-09-30</xbrli:instant></xbrli:period><xbrli:scenario><xbrldi:typedMember dimension="in-capmkt:OngoingTaxLitigationsOrDisputesAxis"><in-capmkt:OngoingTaxLitigationsOrDisputesDomain>OngoingTaxLitigationsOrDisputesDomain1</in-capmkt:OngoingTaxLitigationsOrDisputesDomain></xbrldi:typedMember></xbrli:scenario></xbrli:context><xbrli:context id="I_OngoingTaxLitigationsOrDisputes2"><xbrli:entity><xbrli:identifier scheme="https://www.sebi.gov.in/in-capmkt/Symbol">ARUNAYA</xbrli:identifier></xbrli:entity><xbrli:period><xbrli:instant>2025-09-30</xbrli:instant></xbrli:period><xbrli:scenario><xbrldi:typedMember dimension="in-capmkt:OngoingTaxLitigationsOrDisputesAxis"><in-capmkt:OngoingTaxLitigationsOrDisputesDomain>OngoingTaxLitigationsOrDisputesDomain2</in-capmkt:OngoingTaxLitigationsOrDisputesDomain></xbrldi:typedMember></xbrli:scenario></xbrli:context><xbrli:unit id="pure"><xbrli:measure>xbrli:pure</xbrli:measure></xbrli:unit><in-capmkt:ScripCode contextRef="MainI">000000</in-capmkt:ScripCode><in-capmkt:Symbol contextRef="MainI">ARUNAYA</in-capmkt:Symbol><in-capmkt:MSEISymbol contextRef="MainI">NOTLISTED</in-capmkt:MSEISymbol><in-capmkt:ISIN contextRef="MainI">INE0TTG01017</in-capmkt:ISIN><in-capmkt:NameOfTheCompany contextRef="MainI">ARUNAYA ORGANICS LIMITED</in-capmkt:NameOfTheCompany><in-capmkt:DateOfStartOfFinancialYear contextRef="MainI">2025-04-01</in-capmkt:DateOfStartOfFinancialYear><in-capmkt:DateOfEndOfFinancialYear contextRef="MainI">2026-03-31</in-capmkt:DateOfEndOfFinancialYear><in-capmkt:ReportingQuarter contextRef="MainI">Half Yearly</in-capmkt:ReportingQuarter><in-capmkt:DateOfEndOfReportingPeriod contextRef="MainI">2025-09-30</in-capmkt:DateOfEndOfReportingPeriod><in-capmkt:TypeOfCompany contextRef="MainD">SME</in-capmkt:TypeOfCompany><in-capmkt:WhetherPartAOfAnnexureIOfTheSEBICircularDated31December2024RelatedToComplianceReportOnCorporateGovernanceIsApplicableToTheEntity contextRef="MainD">false</in-capmkt:WhetherPartAOfAnnexureIOfTheSEBICircularDated31December2024RelatedToComplianceReportOnCorporateGovernanceIsApplicableToTheEntity><in-capmkt:ReasonForPartAOfAnnexureIOfTheSEBICircularDated31December2024RelatedToComplianceReportOnCorporateGovernanceIsNotApplicableToTheEntity contextRef="MainD">The Arunaya Organics Limited is listed on the NSE SME EMERGE PLATFORM and therefore, pursuant to the sub-regulation (2) of the Regulations 15 of the SEBI (Listing Obligations and Disclsoure Requirements) Regulations, 2015, the compliance with the Corporate Governance provisions as specified in Regulations 17 (17A), 18, 19, 20, 21, 22, 23, 24, (24A), 25, 26, (26A), 27 and clauses (b) to (i) and (t) of sub-regulation (2) of Regulation 46 and para C, D and E of Schedule V shall not apply.</in-capmkt:ReasonForPartAOfAnnexureIOfTheSEBICircularDated31December2024RelatedToComplianceReportOnCorporateGovernanceIsNotApplicableToTheEntity><in-capmkt:WhetherPartBOfAnnexureIOfTheSEBICircularDated31December2024RelatedToInvestorGrievanceRedressalReportIsApplicableToTheEntity contextRef="MainD">true</in-capmkt:WhetherPartBOfAnnexureIOfTheSEBICircularDated31December2024RelatedToInvestorGrievanceRedressalReportIsApplicableToTheEntity><in-capmkt:WhetherPartCOfAnnexureIOfTheSEBICircularDated31December2024RelatedToDisclosureOfAcquisitionOfSharesOrVotingRightsInUnlistedCompaniesIsApplicableToTheEntity contextRef="MainD">false</in-capmkt:WhetherPartCOfAnnexureIOfTheSEBICircularDated31December2024RelatedToDisclosureOfAcquisitionOfSharesOrVotingRightsInUnlistedCompaniesIsApplicableToTheEntity><in-capmkt:ReasonForPartCOfAnnexureIOfTheSEBICircularDated31December2024RelatedToDisclosureOfAcquisitionOfSharesOrVotingRightsInUnlistedCompaniesIsNotApplicableToTheEntity contextRef="MainD">Not applicable as there was no acquisition of shares or voting rights in Unlisted companies by the Company during the half year ended on 30th September, 2025</in-capmkt:ReasonForPartCOfAnnexureIOfTheSEBICircularDated31December2024RelatedToDisclosureOfAcquisitionOfSharesOrVotingRightsInUnlistedCompaniesIsNotApplicableToTheEntity><in-capmkt:WhetherPartDOfAnnexureIOfTheSEBICircularDated31December2024RelatedToDisclosureOfImpositionOfFineOrPenaltyIsApplicableToTheEntity contextRef="MainD">true</in-capmkt:WhetherPartDOfAnnexureIOfTheSEBICircularDated31December2024RelatedToDisclosureOfImpositionOfFineOrPenaltyIsApplicableToTheEntity><in-capmkt:WhetherPartEOfAnnexureIOfTheSEBICircularDated31December2024RelatedToDisclosureOfUpdatesToOngoingTaxLitigationsOrDisputesIsApplicableToTheEntity contextRef="MainD">true</in-capmkt:WhetherPartEOfAnnexureIOfTheSEBICircularDated31December2024RelatedToDisclosureOfUpdatesToOngoingTaxLitigationsOrDisputesIsApplicableToTheEntity><in-capmkt:WhetherPartFOfAnnexureIOfTheSEBICircularDated31December2024RelatedToDisclosureOfLoansOrGuaranteesOrComfortLettersOrSecuritiesEtcIsApplicableToTheEntity contextRef="MainD">false</in-capmkt:WhetherPartFOfAnnexureIOfTheSEBICircularDated31December2024RelatedToDisclosureOfLoansOrGuaranteesOrComfortLettersOrSecuritiesEtcIsApplicableToTheEntity><in-capmkt:ReasonForPartFOfAnnexureIOfTheSEBICircularDated31December2024RelatedToDisclosureOfLoansOrGuaranteesOrComfortLettersOrSecuritiesEtcIsNotApplicableToTheEntity contextRef="MainD">Not Applicable</in-capmkt:ReasonForPartFOfAnnexureIOfTheSEBICircularDated31December2024RelatedToDisclosureOfLoansOrGuaranteesOrComfortLettersOrSecuritiesEtcIsNotApplicableToTheEntity><in-capmkt:IsSCORESIDAvailable contextRef="MainI">true</in-capmkt:IsSCORESIDAvailable><in-capmkt:SCORESRegistrationID contextRef="MainI">coma01253</in-capmkt:SCORESRegistrationID><in-capmkt:TypeOfSubmission contextRef="MainI">Original</in-capmkt:TypeOfSubmission><in-capmkt:NoOfInvestorComplaints contextRef="PY_I" decimals="0" unitRef="pure">0</in-capmkt:NoOfInvestorComplaints><in-capmkt:NoOfInvestorComplaintsReceivedDuringThePeriod contextRef="MainD" decimals="0" unitRef="pure">0</in-capmkt:NoOfInvestorComplaintsReceivedDuringThePeriod><in-capmkt:NoOfInvestorComplaintsDisposedOffDuringThePeriod contextRef="MainD" decimals="0" unitRef="pure">0</in-capmkt:NoOfInvestorComplaintsDisposedOffDuringThePeriod><in-capmkt:NoOfInvestorComplaints contextRef="MainI" decimals="0" unitRef="pure">0</in-capmkt:NoOfInvestorComplaints><in-capmkt:NoOfInvestorComplaintsDuringThePeriod contextRef="MainD" decimals="0" unitRef="pure">0</in-capmkt:NoOfInvestorComplaintsDuringThePeriod><in-capmkt:NameOfTheAuthority contextRef="I_ImpositionOfFineOrPenalty1">National Stock Exchange of India Limited</in-capmkt:NameOfTheAuthority><in-capmkt:NatureAndDetailsOfTheActionTakenOrOrderPassed contextRef="I_ImpositionOfFineOrPenalty1">NSE through email vide letter dated 12.09.2025 has imposed fine of Rs. 1,41,600 (inc. GST) on the Company for delayed in submission of  Statement of Impact on Audit Qualification a/w the submission of Audited Financial Results of the Company for the year ended 31.03.2025. The Company has submitted the reply to the stock exchange for the waiver of fine which is not considered by the stock exchange. The Company shall make the payment of the fine within the timelines prescribed by NSE.</in-capmkt:NatureAndDetailsOfTheActionTakenOrOrderPassed><in-capmkt:DateOfReceiptOfDirectionOrOrderIncludingAnyAdInterimOrInterimOrdersOrAnyOtherCommunicationFromTheAuthority contextRef="I_ImpositionOfFineOrPenalty1">2025-09-12</in-capmkt:DateOfReceiptOfDirectionOrOrderIncludingAnyAdInterimOrInterimOrdersOrAnyOtherCommunicationFromTheAuthority><in-capmkt:DetailsOfTheViolationOrContraventionCommittedOrAllegedToBeCommitted contextRef="I_ImpositionOfFineOrPenalty1">Delay in submission of Statement of Impact on Audit Qualification a/w the submission of Audited Financial Results of the Company for the year ended 31.03.2025 as defined under the Regulation 33 of the SEBI (Listing Obligations and Disclosure Requirements) Regulations, 2015.</in-capmkt:DetailsOfTheViolationOrContraventionCommittedOrAllegedToBeCommitted><in-capmkt:ImpactOnFinancialOrOperationOrOtherActivitiesOfTheListedEntityQuantifiableInMonetaryTermsToTheExtentPossible contextRef="I_ImpositionOfFineOrPenalty1">There is no impact on the financial, operation or other activities of the Company due to levy of the said fine.</in-capmkt:ImpactOnFinancialOrOperationOrOtherActivitiesOfTheListedEntityQuantifiableInMonetaryTermsToTheExtentPossible><in-capmkt:NameOfTheOpposingParty contextRef="I_OngoingTaxLitigationsOrDisputes1">Income Tax Authority</in-capmkt:NameOfTheOpposingParty><in-capmkt:DateOfInitiationOfTheLitigationDispute contextRef="I_OngoingTaxLitigationsOrDisputes1">2022-03-24</in-capmkt:DateOfInitiationOfTheLitigationDispute><in-capmkt:StatusOfTheLitigationDisputeAsPerLastDisclosure contextRef="I_OngoingTaxLitigationsOrDisputes1">The Company has filed an Appeal before the Commissioner of Income-Tax (Appeals) under Section 246A of the Act and has deposited an amount of ₹ 5.2 lakhs due to which a stay has been granted by the said Commissioner.</in-capmkt:StatusOfTheLitigationDisputeAsPerLastDisclosure><in-capmkt:CurrentStatusOfTheLitigationOrDispute contextRef="I_OngoingTaxLitigationsOrDisputes1">The said case is sub-judice.</in-capmkt:CurrentStatusOfTheLitigationOrDispute><in-capmkt:NameOfTheOpposingParty contextRef="I_OngoingTaxLitigationsOrDisputes2">Income Tax Authority</in-capmkt:NameOfTheOpposingParty><in-capmkt:DateOfInitiationOfTheLitigationDispute contextRef="I_OngoingTaxLitigationsOrDisputes2">2022-03-24</in-capmkt:DateOfInitiationOfTheLitigationDispute><in-capmkt:StatusOfTheLitigationDisputeAsPerLastDisclosure contextRef="I_OngoingTaxLitigationsOrDisputes2">The Company has filed an Appeal before the Commissioner of Income-Tax (Appeals) under Section 246A of the Act and has deposited an amount of ₹ 4.08 lakhs due to which a stay has  been granted by the said Commissioner. The Appeal is pending for further steps/hearing.</in-capmkt:StatusOfTheLitigationDisputeAsPerLastDisclosure><in-capmkt:CurrentStatusOfTheLitigationOrDispute contextRef="I_OngoingTaxLitigationsOrDisputes2">The said case is sub-judice.</in-capmkt:CurrentStatusOfTheLitigationOrDispute></xbrli:xbrl>