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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2021-03-11</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001718852</issuerCik>
        <issuerName>Prometheus Biosciences, Inc.</issuerName>
        <issuerTradingSymbol>RXDX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000792990</rptOwnerCik>
            <rptOwnerName>NESTLE SA</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>AVENUE NESTLE 55</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CH-1800, VEVEY</rptOwnerCity>
            <rptOwnerState>V8</rptOwnerState>
            <rptOwnerZipCode></rptOwnerZipCode>
            <rptOwnerStateDescription>SWITZERLAND</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001803539</rptOwnerCik>
            <rptOwnerName>Societe des Produits Nestle S.A.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>AVENUE NESTLE 55</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CH-1800, VEVEY</rptOwnerCity>
            <rptOwnerState>V8</rptOwnerState>
            <rptOwnerZipCode></rptOwnerZipCode>
            <rptOwnerStateDescription>SWITZERLAND</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series C Convertible Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2500000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series D-1 Convertible Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F2"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>508885</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series D-2 Convertible Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F3"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>721956</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Shares of Series C Preferred Stock are convertible at any time, at the holder's election, at a ratio of ten-for-one share of the Issuer's common stock. In addition, effective immediately prior to the closing of the Issuer's initial public offering of its common stock, each share of Series C Preferred Stock will automatically convert at the ratio of ten-for-one share of the Issuer's common stock. The Series C Preferred Stock has no expiration date.</footnote>
        <footnote id="F2">Shares of Series D-1 Preferred Stock are convertible at any time, at the holder's election, at a ratio of ten-for-one share of the Issuer's common stock. In addition, effective immediately prior to the closing of the Issuer's initial public offering of its common stock, each share of Series D-1 Preferred Stock will automatically convert at the ratio of ten-for-one share of the Issuer's common stock. The Series D-1 Preferred Stock has no expiration date.</footnote>
        <footnote id="F3">Shares of Series D-2 Preferred Stock are convertible at any time, at the holder's election, at a ratio of ten-for-one share of the Issuer's common stock. In addition, effective immediately prior to the closing of the Issuer's initial public offering of its common stock, each share of Series D-2 Preferred Stock will automatically convert at the ratio of ten-for-one share of the Issuer's common stock. The Series D-2 Preferred Stock has no expiration date.</footnote>
        <footnote id="F4">The shares reported herein represent, (i) 855,000 shares of Series C Preferred Stock held by Nestle Health Science US Holdings, Inc. (&quot;NHS&quot;), (ii) 508,885 shares of Series D-1 Preferred Stock held by NHS, (iii) 721,956 shares of Series D-2 Preferred Stock held by NHS and (iv) 1,645,000 shares of Series C Preferred Stock held by Societe des Produits Nestle S.A. (&quot;SPN&quot;). NHS is a wholly owned subsidiary of NIMCO US, Inc. (&quot;NIMCO&quot;). NIMCO, in turn, is a wholly-owned subsidiary of Nestle US Holdco, Inc. (&quot;Nestle US Holdco&quot;), which is a wholly-owned subsidiary of SPN. The ultimate parent company of NHS, NIMCO, Nestle US Holdco and SPN is Nestle S.A. (&quot;Nestle&quot;). Each of these entities may be deemed to share voting and investment power with respect to all shares of Series C Preferred Stock, Series D-1 Preferred Stock and Series D-2 Preferred Stock held by NHS.</footnote>
        <footnote id="F5">(Continued from Footnote 4) Additionally, Nestle may be deemed to share voting and investment power with respect to all shares of Series C Preferred Stock held by SPN.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>SOCIETE DES PRODUITS NESTLE S.A. By: /s/ Claudio Kuoni, Name: Claudio Kuoni, Title: Vice President</signatureName>
        <signatureDate>2021-03-11</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>NESTLE S.A. By: /s/ Gregory Behar, Name: Gregory Behar, Title: Deputy Executive Vice President</signatureName>
        <signatureDate>2021-03-11</signatureDate>
    </ownerSignature>
</ownershipDocument>
