Various embodiments for repository management in a data deduplication system, by a processor device, are provided. Metadata of an inode structure of an entire pre-allocated file system is captured, exported, and compressed from an existing deduplication appliance, the pre-allocated file system comprising a fully padded file system. The exported and compressed metadata of the pre-allocated file system is decompressed and imported into a data deduplication repository of a new deduplication appliance having an identical file system size as within the existing deduplication appliance, to initially configure or subsequently scale the inode structure of a file system of the data deduplication repository of the new deduplication appliance efficiently.