The main objective of the current Special Section is to collect, formally present and discuss the most recent and relevant advances in control-oriented modeling and validation, system diagnosis and advanced control design of complex energy conversion systems based on fuel cells. Moreover, the Special Section is also focused on providing the researchers and engineers with the state-of-art research and guidelines in these important fields for the next years. In total, the Special Session is composed by 17 contributions covering the research in theoretical aspects related to modelling, diagnosis and control applied to energy management systems based on fuel cells or considering fuel cells as part of overall hybrid systems.