Systems and methods for performing application aware backups and/or generating other application aware secondary copies of virtual machines are described. For example, the systems and methods described herein may access a virtual machine, automatically discover various databases and/or applications (e.g., SQL, Exchange, Sharepoint, Oracle, and so on) running on the virtual machine, and perform data storage operations that generate a backup, or other secondary copy, of the virtual machine, as well as backups, or other secondary copies, of each of the discovered applications.