A method for configuration of an Auxiliary Processing Unit (APU) of multiprocessor system is presented. The multiprocessor system has at least a Main Processing Unit (MPU) coupled to the APU via a communication link. The APU has at least a first memory and a second memory. The method includes a plurality of steps. At step the first memory is divided into an application sector, a boot sector and a common sector. At another step interrupts of the APU except interrupt/s that is/are being received via the communication link are disabled. At a further step interrupt vector/s pertaining to the communication link is/are mapped to the boot sector of the first memory. At another step a configuration code is received selectively into the application sector of the first memory and into the second memory. At a further step the interrupt/s that is/are being received via the communication link are disabled. At a further step the common sector of the first memory is updated from the second memory.