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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3/A</documentType>

    <periodOfReport>2016-02-10</periodOfReport>

    <dateOfOriginalSubmission>2016-02-10</dateOfOriginalSubmission>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001445283</issuerCik>
        <issuerName>PROTEOSTASIS THERAPEUTICS, INC.</issuerName>
        <issuerTradingSymbol>PTI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001565579</rptOwnerCik>
            <rptOwnerName>PERRIGO SCIENCE ONE LTD.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>TREASURY BUILDING</rptOwnerStreet1>
            <rptOwnerStreet2>LOWER GRAND CANAL STREET</rptOwnerStreet2>
            <rptOwnerCity>DUBLIN</rptOwnerCity>
            <rptOwnerState>L2</rptOwnerState>
            <rptOwnerZipCode>2</rptOwnerZipCode>
            <rptOwnerStateDescription>IRELAND</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000737186</rptOwnerCik>
            <rptOwnerName>PERRIGO CORP LTD.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>TREASURY BUILDING,</rptOwnerStreet1>
            <rptOwnerStreet2>LOWER GRAND CANAL STREET</rptOwnerStreet2>
            <rptOwnerCity>DUBLIN</rptOwnerCity>
            <rptOwnerState>L2</rptOwnerState>
            <rptOwnerZipCode>2</rptOwnerZipCode>
            <rptOwnerStateDescription>IRELAND</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001307004</rptOwnerCik>
            <rptOwnerName>ELAN PHARMA INTERNATIONAL LTD.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>TREASURY BUILDING,</rptOwnerStreet1>
            <rptOwnerStreet2>LOWER GRAND CANAL STREET</rptOwnerStreet2>
            <rptOwnerCity>DUBLIN</rptOwnerCity>
            <rptOwnerState>L2</rptOwnerState>
            <rptOwnerZipCode>2</rptOwnerZipCode>
            <rptOwnerStateDescription>IRELAND</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001323996</rptOwnerCik>
            <rptOwnerName>PERRIGO HOLDINGS LTD.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>TREASURY BUILDING,</rptOwnerStreet1>
            <rptOwnerStreet2>LOWER GRAND CANAL STREET</rptOwnerStreet2>
            <rptOwnerCity>DUBLIN</rptOwnerCity>
            <rptOwnerState>L2</rptOwnerState>
            <rptOwnerZipCode>2</rptOwnerZipCode>
            <rptOwnerStateDescription>IRELAND</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001585364</rptOwnerCik>
            <rptOwnerName>PERRIGO Co plc</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>TREASURY BUILDING,</rptOwnerStreet1>
            <rptOwnerStreet2>LOWER GRAND CANAL STREET</rptOwnerStreet2>
            <rptOwnerCity>DUBLIN</rptOwnerCity>
            <rptOwnerState>L2</rptOwnerState>
            <rptOwnerZipCode>2</rptOwnerZipCode>
            <rptOwnerStateDescription>IRELAND</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable></nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series A Convertible Redeemable 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>2416612</value>
                    <footnoteId id="F1"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B Convertible Redeemable 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>366455</value>
                    <footnoteId id="F3"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The Series A Convertible Redeemable Preferred Stock (the &quot;Series A Shares&quot;) are convertible on a 10.8102-to-1 basis into the Issuer's Common Stock at any time at the election of the Reporting Person and will automatically convert, together with the accrued but unpaid dividends, upon closing of the Issuer's initial public offering into the number of shares of the Issuer's Common Stock shown in column 3.  The Series A Shares do not have an expiration date.</footnote>
        <footnote id="F2">Perrigo Science One Ltd. (&quot;Science&quot;) (formerly Elan Science One Ltd.) is the direct owner of these securities.  Science is a direct or indirect, wholly-owned subsidiary of each of the other reporting persons.</footnote>
        <footnote id="F3">The Series  B Convertible Redeemable Preferred Stock (the &quot;Series B Shares&quot;) are convertible on a 10.8102-to-1 basis into the number of shares of the Issuer's Common Stock as shown in column 3 at any time at the election of the Reporting Person and will automatically convert upon the closing of the Issuer's initial public offering.  The Series B Shares do not have an expiration date.</footnote>
    </footnotes>

    <remarks>This form amends and restates the Form 3 previously filed to reflect the change in name of Elan Science One Ltd. to Perrigo Science One Ltd. and to add each of Perrigo Company plc, Perrigo Holdings Ltd., Elan Pharma International Limited and Perrigo Corporation Limited as additional reporting persons. The additional reporting persons are the direct and indirect parents of Science.</remarks>

    <ownerSignature>
        <signatureName>/s/Todd Kingma, Secretary of Perrigo Science One Ltd.</signatureName>
        <signatureDate>2016-02-18</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/Todd Kingma, Secretary of Perrigo Corporation Limited</signatureName>
        <signatureDate>2016-02-18</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/Todd Kingma, Director of Elan Pharma International Limited</signatureName>
        <signatureDate>2016-02-18</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/Todd Kingma, Secretary of Perrigo Holdings Ltd.</signatureName>
        <signatureDate>2016-02-18</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/Todd Kingma, Secretary of Perrigo Company plc</signatureName>
        <signatureDate>2016-02-18</signatureDate>
    </ownerSignature>
</ownershipDocument>
