A method and apparatus is disclosed herein for maintaining deduplication metadata on disk separate from an in-memory deduplication file system for a deduplication computing system. The method may include reading deduplication metadata from a first memory of a deduplication computing system. Furthermore, the method may include maintaining deduplicated data for a file system in a second memory, and maintaining the deduplication metadata that describes the deduplicated data of the file system in the first memory of the deduplication computing system, wherein the first memory is a different type of memory and separated from the second memory in the deduplication computing system. Furthermore, the method may include accessing the deduplication metadata in the second memory in response to receipt of a request by the deduplication computing system to perform a first operation with deduplicated data of the file system in the second memory.