One embodiment provides a method for re-balancing data and metadata across multiple sub-file systems of a file system. The method includes determining sub-file systems including an amount of data that exceeds a threshold. At least one cell in the sub-file systems is identified as a candidate for re-balancing. A re-balance process is performed on the at least one cell that includes performing a flush operation to flush dirty data from file system buffers, copying an inode table for an independent set of files in the at least one cell to a destination sub-file system, notifying an allocation manager for the destination sub-file system of a new storage pool to manage, and performing an un-quiesce operation on I/O operations to each element in the at least one cell.