A system and method for providing secondary-factor authentication with a third party application that can include enrolling a device application instance of an account into a secondary-factor authentication service on behalf of a service provider that includes at the secondary-factor authentication service, receiving a secondary factor of authentication enrollment request of an account, the request received from the service provider, transmitting an activation code, and pairing the device application instance with the account through the activation code; receiving an authentication request identifying the account; transmitting an authentication request to the device application instance paired with the account; validating a response to the application request; and transmitting an assessment to the service provider.