Embodiments of the invention address deficiencies of the art in respect to electronic messaging security through replicated certificate stores and provide a method, system and computer program product user-specific certificate repository replication. In one embodiment of the invention, a method of replicating with multiple different messaging systems disposed in correspondingly different computing clients, retrieving a local repository of untrusted certificates from each of the different messaging systems during replication, and associating each retrieved local repository with a particular end user can be provided. Moreover, the method can include updating a global repository of untrusted certificates with the untrusted certificates of each local repository while eliminating redundant instances of an untrusted certificate present in different retrieved local repositories.