Hypervisor agnostic interchangeable backup recovery and file level recovery from virtual disks

Provided are a computer program product, system, and method for hypervisor agnostic interchangeable backup recovery and file level recovery from virtual disks. Data is stored for a first virtual disk that represents data in a first format and metadata for the first virtual disk in a common data format in a storage having a fixed block length. A virtual disk file represents data in a second format that allows variable size blocks. Multiple instances of the fixed block length of blocks of data for the second virtual disk indicated in the virtual disk file are read. Each instance of the read fixed block length of blocks is written to the storage in the common data format with metadata describing the format of the blocks in the second virtual disk, and can be restored to a third virtual disk in the first or second format.