A method of configuring a device having programmable logic is disclosed. The method comprises storing instructions in the device; selecting between one of the instructions stored in the device and an instruction coupled to an input/output port of the device; coupling the instruction to a non-volatile memory; and reading a configuration bitstream from the non-volatile memory based upon the selected instruction. A method of enabling a multi-boot configuration of a device having programmable logic is disclosed. The method comprises powering up the device using a first configuration bitstream from a first type of configuration device in response to a first command; receiving a reboot command; and reconfiguring the device using a second configuration bitstream from a second type of configuration device in response to a second command which is different than the first command. Circuits enabling a multi-boot configuration of a device having programmable logic are also disclosed.