A flash-based programmable integrated circuit includes programmable circuitry, a flash memory array coupled to the programmable circuitry for configuring it, flash programming circuitry for programming the flash memory array, and an on-chip intelligence, such as a microcontroller or state machine, coupled to the programming circuitry to program the flash memory from off-chip data supplied via an I/O pad, or to refresh the data stored in the flash memory to prevent it from degrading.