Provided are a system and article of manufacture for merging metadata on files in a backup storage. A query is received for information on files from a file system for a client node. A determination is made of metadata for files in a backup storage for the client node stored external to backup sets. At least one backup set in the backup storage for the client node is processed to determine metadata for files included in at least one backup set. The determined metadata for files in the backup storage and for files included in at least one backup set is merged to form merged metadata. The query is executed against the merged metadata to determine files whose metadata satisfies the query. Results including information from the merged metadata on the determined files are returned.