In this paper, the optimal and safe operation of a hybrid power system based on a fuel cell system and renewable energy sources is analyzed. The needed DC power resulting from the power flow balance on the DC bus is ensured by the FC system via the air regulator or the fuel regulator controlled by the power-tracking control reference or both regulators using a switched mode of the above-mentioned reference. The optimal operation of a fuel cell system is ensured by a search for the maximum of multicriteria-based optimization functions focused on fuel economy under perturbation, such as variable renewable energy and dynamic load on the DC bus. Two search controllers based on the global extremum seeking scheme are involved in this search via the remaining fueling regulator and the boost DC–DC converter. Thus, the fuel economy strategies based on the control of the air regulator and the fuel regulator, respectively, on the control of both fueling regulators are analyzed in this study. The fuel savings compared to fuel consumed using the static feed-forward control are 6.63%, 4.36% and 13.72%, respectively, under dynamic load but without renewable power. With renewable power, the needed fuel cell power on the DC bus is lower, so the fuel cell system operates more efficiently. These percentages are increased to 7.28%, 4.94% and 14.97%.