A system and method for automatic key and certificate management is disclosed. In particular, a key store in a base computer contains both new and previously viewed cryptographic keys. When a mobile communications device is to be updated with the new keys, the new keys are automatically identified by comparing the keys stored in the base computer with a list of previously viewed keys to determine which new keys are to be marked for download. Upon marking the new keys, the user may be prompted to download the newly identified keys, or they may be downloaded automatically. Once the new keys have been marked, the list of previously viewed keys is updated to include those marked, so that the next time updating occurs, the previously viewed key list will be correct.