A system and method for maintaining checkpoints of a keyed data structure using a sequential log are provided. The system and method are built upon the idea of writing all updates to a keyed data structure in a physically sequential location. The system and method make use of a two-stage operation. In a first stage, various values of the same key are combined such that only the latest value in a given checkpoint interval is maintained for writing to persistent storage. In a second stage of the operation, a periodic write operation is performed to actually store the latest values for the key-value pairs to a persistent storage. All such updates to key-value pairs are written to the end of a sequential log. This minimizes the physical storage input/output (I/O) overhead for the write operations. Data structures are provided for identifying the most current entries in the sequential log for each key-value pair.