One embodiment of the present invention discloses a two-phase configuration process (“TCP”) to configure a field-programmable gate array (“FPGA”) to include a configurable microcontroller unit (“CMU”) during a phase I configuration and configuring the CMU during a phase II configuration. TCP, in one aspect, is able to receive first configuration data from a first external storage location via a communication bus. After storing the first configuration data in a first configuration memory for configuring FPGA to contain a CMU for the phase I configuration, second configuration data with MCU attributes is obtained from a second external storage location via the communication bus. The second configuration data is subsequently stored in a second configuration memory for programming the CMU for the phase II configuration.