A device includes a loop port controlled by a loop initialization procedure in response to control flags. The device includes a programmable controller and a fibre channel loop port including a transmitter, a receiver, and a port control circuit. The port control circuit controls the loop initialization procedure in response to control flags set by the programmable controller. Methods of performing loop initialization in a loop port include initializing a loop initialization protocol (LIP) hardware state machine, controlling LIP operations with the LIP hardware state machine, determining if control of the loop initialization operations should be transferred to a programmable controller in response to a predetermined loop initialization event, and if so, transferring control of the loop initialization operations to the programmable controller.