The invention relates to a method and to a system for operating a fuel cell system (22) and at least one sub-system (30) of the fuel cell system (22). According to the invention, these are arranged in a vehicle (10), wherein the energy for a drive train (12) of the vehicle (10) can be drawn both from the fuel cell system (22) and from an alternative energy store (26). The method comprises the following method steps: first, the number and duration of shut-down and/or stop phases of the vehicles (10) in a defined time interval in a first vehicle state (86) or in a second vehicle state (88) is determined based on vehicle state-specific learning functions (90, 112). Operating parameters of the fuel cell system (22) and of the at least one sub-system (30) of the fuel cell system (22) are then adjusted in dependence on the determined number and duration of shut-down and/or stop phases of the vehicle (10).