System and method to exclude unsupported disks during application consistent backups

A data protection agent is installed within a virtual machine (VM). A request to perform a backup is received. The request includes identifications of virtual machine disks (VMDKs) associated with the virtual machine. Communications are exchanged with a disk manager of a guest operating system of the VM to generate a map that maps the VMDKs to volumes attached to the VM. Communications are exchanged with an application in the VM to be protected to identify which of the volumes contain application databases associated with the application. A copy service is instructed to prepare the application for backup. A request is issued to a snapshot data mover for a snapshot of the application. The snapshot request includes identifications of a subset of the VMDKs mapped to corresponding volumes that contain the application databases. VMDKs mapped to corresponding volumes not containing the application databases are excluded from the snapshot request.