A method for controlling a fuel cell (12) includes the following steps: measuring the fluid pressure in a first compartment from the anode and cathode compartments of the fuel cell (12); calculating a first target pressure for the fluid pressure in the second compartment of the fuel cell (12), the first target pressure depending on the fluid pressure measured in the first compartment; stabilizing the fluid pressure in the second compartment to the first target pressure; measuring the fluid pressure in the second compartment; calculating a second target pressure for the fluid pressure in the first compartment, the second target pressure depending on the fluid pressure measured in the second compartment; and stabilizing the fluid pressure in the first compartment at the second target pressure.