Methods, systems, and media for controlling append-only file rewrites are provided. In accordance with some embodiments, the methods comprising: determining a utilization of a shard of a database; determining whether the utilization exceeds a persistent storage utilization threshold; determining a recovery time to recover the shard from an append-only file; determining whether the recovery time exceeds a recovery time threshold; and when the utilization is determined to exceed the utilization threshold or when the recovery time is determined to exceed the recovery time threshold, causing an append-only-file rewrite to be performed.