The research presented in this chapter deals with the design and implementation of Real-Time (RT) control systems applying advanced Field Programmable Gate Array (FPGAs). The chapter proposes a promising flexible architecture that uses RT Operating System (RTOS) and ready-to-use Intellectual Properties (IPs). The authors detail an approach that uses software closed control loop function blocks (FB), running on embedded processor cores. These FBs implement the different control drive sub-modules into RTOS tasks of the execution environment, where each task has to be executed under well defined conditions. Two RTOSes are evaluated: µC-OS/II and Xilkernel. The FPGA embedded processor cores are combined with reconfigurable logic and dedicated resources on the FPGA. This System-on-Chip (SoC) has been applied to electric motors drive. A comparative analysis, in terms of speed and cost, is carried-out between various hardware/software FPGA-based architectures, in order to enhance flexibility without sacrificing performance and increasing cost. Case studies results validate successfully the feasibility and the efficiency of the flexible approach for new and more complex control algorithms. The performance and flexibility of FPGA-based motor controllers are enhanced with the reliability and modularity of the introduced RTOS support.