This work aims to develop a novel system, including software and hardware, to perform independent control tasks in a genuine parallel manner. Currently, to control processes with various sampling periods, distributed control systems are most commonly utilized. The main goal of this system is to propose an alternative solution, which allows simultaneous control of both fast and slow processes. The presented approach utilizes FPGA (Field Programmable Gate Array) with Nios II processor (Intel Soft Processor Series) to implement and maintain instances of independent controllers. Instances can implement FDMC (Fast Dynamic Matrix Control) and PID (Proportional-Integral-Derivative) control algorithms with various sampling times. The FPGA-based design allows for true independence of controllers’ execution both from one another and the managing processor. Also, pure parallel execution allows for implementing slow and fast controllers in the same device. The complete flexible system with a matrix of controllers working in parallel in real-time was tested with both simulated and actual control processes (servomotor), yielding the same results as fully simulated experiments.