This paper presents a methodology to design and prototype FPGA-based fully digital controller for power electronics systems. A Top-down design methodology is used to study step by step the digital adaptation and the fully digital implementation of the control algorithm. Finally, “FPGA in the loop” prototyping is achieved, based on MATLAB/SimPower Systems and Altera DSP Builder computer aided design tools. Modeling, simulation and FPGA in the loop prototyping are achieved in a unique design environment. An application using the proposed methodology is studied: a fully digital controller for a three-phase parallel active power filter. The fully digital controller implementation is described and the hardware digital controller experimentally validated by FPGA in the loop prototyping