Scheduling methods of phased garbage collection and housekeeping operations in a flash memory system

An embodiment of a non-volatile memory storage system comprises a memory controller, and a flash memory module. The memory controller manages the storage operations of the flash memory module. The memory controller is configured to assign a priority level to one or more types of house keeping operations that may be higher than a priority level of one or more types of commands received by a host coupled to the storage system, and to service all operations required of the flash memory module according to priority.