A variety of currently operational GNSS frequencies and rapid development of new navigation satellite systems resulted in the need for interoperability and compatibility. Recent state-of-the-art integrated GNSS front-ends are capable of simultaneous support of multiple navigation systems [1,2]. A unification of the signal processing part is also possible and, what is more, desirable. This paper introduces a proposal for universal instruction set extension (ISE), which is used for accelerating signal processing in SDR (Software Defined Radio) based GNSS applications. The results of this work were implemented and tested on the chip multithreading general purpose processor -AGATE [3], running on the Xilinx Virtex-6 ML605 FPGA evaluation board.