Synchronization of metadata-based system snapshots with a state of user data is presented herein. A snapshot component can generate, at respective times, snapshots of roots of respective trees of a system—the respective trees comprising metadata representing respective states of the system corresponding, via the snapshots, to the respective times. Further, a garbage collection component can select a snapshot of the snapshots of the roots that is older than remaining snapshots of the snapshots of the roots, and determine, using an object table of the snapshot referencing data chunks comprising respective objects of the system, whether a data chunk of the data chunks comprises an inactive object of the respective objects to facilitate a selection of the data chunk as a garbage collection (GC) candidate for deletion via a GC procedure.