<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2019-02-28</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001701114</issuerCik>
        <issuerName>Blue Apron Holdings, Inc.</issuerName>
        <issuerTradingSymbol>APRN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001192929</rptOwnerCik>
            <rptOwnerName>FOX KENNETH A</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BLUE APRON HOLDINGS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>40 WEST 23RD STREET</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10010</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>Former Director</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <footnotes></footnotes>

    <remarks>The reporting person resigned as a director of Blue Apron Holdings, Inc., effective February 28, 2019. As a result, the reporting person is no longer subject to Section 16 in connection with his transactions in the equity securities of Blue Apron Holdings, Inc. and therefore will no longer report any such transactions on Form 4 or Form 5.</remarks>

    <ownerSignature>
        <signatureName>/s/ Kenneth A. Fox</signatureName>
        <signatureDate>2019-03-04</signatureDate>
    </ownerSignature>
</ownershipDocument>
