Most motion control systems for mechatronic systems are implemented on digital computers. In this paper we present an FPGA based solution implemented on a low cost Xilinx Spartan III FPGA. A Production Cell setup with multiple parallel operating units is chosen as a test case. The embedded control software for this system is designed in gCSP using a reusable layered CSP based software structure. gCSP is extended with automatic Handel-C code generation for configuring the FPGA. Many motion control systems use floating point calculations for the loop controllers. Low cost general purpose FPGAs do not implement hardware-based floating point units. The loop controllers for this system are converted from floating point to integer based calculations using a stepwise refinement approach. The result is a complete FPGA based motion control system with better performance figures than previous CPU based implementations.