A computer-implemented method for protecting virtual machine data may include (1) receiving a request to perform a granular backup operation on data stored by a guest system within a virtual machine, (2) identifying a storage container that comprises an agent that performs backup operations, (3) attaching the storage container to the virtual machine in response to the request, and (4) performing the granular backup operation by sending an instruction to the guest system within the virtual machine to execute the agent. Various other methods, systems, and computer-readable media are also disclosed.