Abstract In response to the global initiative towards hydrogen energy, increasing focus has been placed on enhancing the performance, reliability and endurance of fuel cells by utilizing advanced control and monitoring strategies. However, due to the multi-variable. multi-loop and multi-physics nature of hydrogen fuel cells, the current decentralized architecture, where fuel cell controllers are isolated and placed in separate enclosures is no longer sufficient to carry out intricate coordinated control strategies. To this end, in this paper, we introduce a novel full-loop architecture, which enables the integration of the fuel cell controller, the air compressor controller, and the power electronics controller within one enclosure, reducing system size and cost. Moreover, based on the integrated hardware architecture, coordinated control such as oxygen/hydrogen pressure coordination can be carried out efficiently. A case study on electrochemical impedance spectroscopy has been conducted, demonstrating the advanced control and monitoring capabilities of this controller architecture.