In one embodiment, an extent store layer of a storage input/output (I/O) stack executing on one or more nodes of a cluster manages efficient logging and checkpointing of metadata. The metadata managed by the extent store layer, i.e., the extent store metadata, resides in a memory (in-core) of each node and is illustratively organized as a key-value extent store embodied as one or more data structures, e.g., a set of hash tables. Changes to the set of hash tables are recorded as a continuous stream of changes to SSD embodied as an extent store layer log. A separate log stream structure (e.g., an in-core buffer) may be associated respectively with each hash table such that changed (i.e., dirtied) slots of the hash table are recorded as entries in the log stream structure. The hash tables are written to SSD using a fuzzy checkpointing technique.