Hello anonymous user, assuming you're talking about Azure AD registered applications then you need to upload the certificate in the Azure AD app registration created for your Server application. For how to load it into your client application token request take a look to Assertion format. Unless you meet the following pre-requisites there's not point using certificate based authentication.
Please let me know if you need more help. If the answer was helpful to you, please accept it and optionally fill the feedback form it so that other members in the community can benefit from it.