The disclosed computer-implemented method for managing security certificates through email may include (1) receiving an encrypted email that contains both identifying information that identifies a security certificate for authenticating a website and a management command relating to the security certificate, (2) determining whether authentication of the encrypted email succeeded such that the management command is authorized, and (3) when a determination is made that authentication of the encrypted email succeeded, identifying the security certificate using the identifying information and executing the management command with respect to the identified security certificate. Various other methods, systems, and computer-readable media are also disclosed.