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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2017-07-05</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001508900</rptOwnerCik>
            <rptOwnerName>Bessemer Venture Partners VIII L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BESSEMER VENTURE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>1865 PALMER AVE., SUITE 104</rptOwnerStreet2>
            <rptOwnerCity>LARCHMONT</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10538</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001508902</rptOwnerCik>
            <rptOwnerName>Bessemer Venture Partners VIII Institutional L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BESSEMER VENTURE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>1865 PALMER AVENUE, SUITE 104</rptOwnerStreet2>
            <rptOwnerCity>LARCHMONT</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10538</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001559306</rptOwnerCik>
            <rptOwnerName>Deer VIII &amp; Co. L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BESSEMER VENTURE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>1865 PALMER AVENUE, SUITE 104</rptOwnerStreet2>
            <rptOwnerCity>LARCHMONT</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10538</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001559311</rptOwnerCik>
            <rptOwnerName>Deer VIII &amp; Co. Ltd.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BESSEMER VENTURE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>1865 PALMER AVENUE, SUITE 104</rptOwnerStreet2>
            <rptOwnerCity>LARCHMONT</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10538</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Series A Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-07-05</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>295546</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class B Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>14777330</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Series B Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F3"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-07-05</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>350153</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class B Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>17507650</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Series C Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-07-05</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>725528</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class B Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>3627640</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Series D Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F5"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-07-05</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>375181</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F5"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class B Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>375181</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Class B Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F6"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-07-05</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F6"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>36287771</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F6"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class A Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>36287771</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>36287771</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F7"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The Series A Preferred Stock converted into Class B Common Stock on a 50:1 basis automatically upon the closing of the issuer's initial public offering of its Class A Common Stock without payment of consideration in an exempt transaction pursuant to Rules 16b-6 and 16b-7. The Series A Preferred Stock was convertible at any time at the holder's election and automatically upon the closing of the issuer's initial public offering of its Class A Common Stock.  The shares had no expiration date.  Prior to the conversion, Bessemer Venture Partners VIII Institutional L.P. (&quot;BVP VIII Inst&quot;) and Bessemer Venture Partners VIII, L.P. (&quot;BVP VIII&quot;, together with BVP VIII Inst referred to collectively, the &quot;Funds&quot;) owned 161,369 shares and 134,177 shares, respectively, of Series A Preferred Stock.</footnote>
        <footnote id="F2">Deer VIII &amp; Co. Ltd. (&quot;Deer Ltd.&quot;) is the general partner of Deer VIII &amp; Co. L.P. (&quot;Deer L.P.&quot;), which is the general partner of each of the Funds. Deer Ltd. and Deer L.P. disclaim beneficial ownership of the securities held by the Funds, and this report shall not be deemed an admission that Deer Ltd. and Deer L.P. are the beneficial owners of such securities, except to the extent of their pecuniary interest therein, if any, by virtue of their direct and indirect general partner interests in the Funds.</footnote>
        <footnote id="F3">The Series B Preferred Stock converted into Class B Common Stock on a 50:1 basis automatically upon the closing of the issuer's initial public offering of its Class A Common Stock without payment of consideration in an exempt transaction pursuant to Rules 16b-6 and 16b-7.  The Series B Preferred Stock was convertible at any time at the holder's election and automatically upon the closing of the issuer's initial public offering of its Class A Common Stock.  The shares had no expiration date. Prior to the conversion, BVP VIII Inst and BVP VIII owned 191,184 shares and 158,969 shares, respectively, of Series B Preferred Stock.</footnote>
        <footnote id="F4">The Series C Preferred Stock converted into Class B Common Stock on a 5:1 basis automatically upon the closing of the issuer's initial public offering of its Class A Common Stock without payment of consideration in an exempt transaction pursuant to Rules 16b-6 and 16b-7.  The Series C Preferred Stock was convertible at any time at the holder's election and automatically upon the closing of the issuer's initial public offering of its Class A Common Stock.  The shares had no expiration date. Prior to the conversion, BVP VIII Inst and BVP VIII owned 396,139 shares and 329,389 shares, respectively, of Series C Preferred Stock.</footnote>
        <footnote id="F5">The Series D Preferred Stock converted into Class B Common Stock on a 1:1 basis automatically upon the closing of the issuer's initial public offering of its Class A Common Stock without payment of consideration in an exempt transaction pursuant to Rules 16b-6 and 16b-7.  The Series D Preferred Stock was convertible at any time at the holder's election and automatically upon the closing of the issuer's initial public offering of its Class A Common Stock.  The shares had no expiration date. As of the date hereof, BVP VIII Inst and BVP VIII own 204,849 shares and 170,332 shares, respectively, of Series D Preferred Stock.</footnote>
        <footnote id="F6">The Class B Common Stock is convertible into the issuer's Class A Common Stock on a one-for-one basis upon certain transfers of such shares and at the holder's election and has no expiration date.</footnote>
        <footnote id="F7">As of the date hereof, BVP VIII Inst and BVP VIII own 19,813,194 shares and 16,474,577 shares, respectively, of Class B Common Stock.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Scott Ring, General Counsel, Deer VIII &amp; Co. Ltd., the General Partner of Deer VIII &amp; Co. L.P., the General Partner of Bessemer Venture Partners VIII L.P.</signatureName>
        <signatureDate>2017-07-07</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Scott Ring, General Counsel, Deer VIII &amp; Co. Ltd., the General Partner of Deer VIII &amp; Co. L.P., the General Partner of Bessemer Venture Partners VIII Institutional L.P.</signatureName>
        <signatureDate>2017-07-07</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Scott Ring, General Counsel, Deer VIII &amp; Co. Ltd., the General Partner of Deer VIII &amp; Co. L.P</signatureName>
        <signatureDate>2017-07-07</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Scott Ring, General Counsel, Deer VIII &amp; Co. Ltd</signatureName>
        <signatureDate>2017-07-07</signatureDate>
    </ownerSignature>
</ownershipDocument>
