A mechanism is provided for cross-allocated block repair in a mounted file system. A set of cross-allocated blocks are identified from a plurality of blocks within an inode of the mounted file system, based on a corresponding bit associated with each cross-allocated block in a duplicated block information bitmap being in a first identified state. The set of cross-allocated blocks are repaired using a user-defined repair process. Then one or more of the set of cross-allocated blocks are deallocated based on results of the user-defined repair process.