1. A system for backing up an encrypted file, the system comprising: a primary storage system; a secondary storage device residing in a secondary storage system; and a data agent implemented in computer hardware of a computing system within the primary storage system, the data agent configured to: receive an indication to backup an encrypted file stored in the primary storage system to the secondary storage device, the encrypted file comprising an encrypted version of a file and a plurality of encrypted keys, wherein a first encrypted key of the plurality of encrypted keys is an encrypted data encryption key assigned to the computing system and a second encrypted key of the plurality of encrypted keys is an encrypted data encryption key assigned to a user; and in response to the indication: extract the first encrypted key from the encrypted file; decrypt the first encrypted key to obtain a copy of a data encryption key; discard the first encrypted key; decrypt the encrypted file using the copy of the data encryption key to obtain a decrypted file; and provide the decrypted file to a secondary storage system for backup to the secondary storage device.