A system is disclosed for pre-registering authentication devices. A security key provider system may receive a request to pre-register a security key with identified applications from an enterprise. Responsive to receiving the request, the security key provider system instructs the security key to generate a unique authentication code for each of the applications. The security key provider system may generate pre-registration information based on the authentication codes and pre-register the authentication codes of the security key to the applications by providing the pre-registration information to the applications on behalf of the enterprise. The security key provider system may instead provide the pre-registration information to the enterprise to allow the enterprise to pre-register the authentication codes.