An apparatus in one embodiment comprises at least one processing device comprising a processor coupled to a memory. The processing device is configured to capture metadata from a metadata area of a storage system for checkpointing, and to store the captured metadata as checkpointed metadata in a user data area of the storage system in association with mapping information relating portions of the checkpointed metadata to particular storage locations in the user data area. The processing device in some embodiments is implemented within the storage system, and may comprise a storage controller of the storage system. The mapping information illustratively comprises a plurality of page location arrays each having a plurality of entries specifying respective locations of checkpointed metadata pages in the user data area. The mapping information may further comprise one or more array location arrays each indexed by a corresponding set of page location array identifiers specifying respective locations of page location arrays in the user data area.