A method to control the heat balance of fuel cell stacks in a fuel cell system, the fuel cell system including at least one fuel cell unit including fuel cell stacks, whose fuel cells include an anode side and a cathode side, as well as an electrolyte interposed therebetween, and a recuperator unit for heat exchange for preheating a supply flow of the cathode side. In the method, a desired portion is separated from the fuel exhaust flow coming from the anode side and adapted to be mixed with the cathode side exit flow before said recuperator unit. Also provided is a fuel cell system implementing the method.