System and method for managing metadata. A computer system includes one or more hosts, each host having an associated backup agent. Each backup agent conveys data from its associated host to a storage pool and stores metadata associated with the data in a metabase. In response to detecting that a first metabase meets a first condition, the system identifies a backup agent that has stored metadata in the first metabase and redistributes at least a portion of the metadata to a second metabase. In one embodiment, the first condition comprises detecting the amount of metadata stored in the first metabase reaching a threshold value. In a further embodiment, the metadata comprises entries, each of which corresponds to a data file. Each entry includes a fingerprint that is derived from and identifies the corresponding data file. The fingerprints identifying the data files may be encrypted.