A fuel cell system includes a fuel cell and a controller that controls a hydrocarbon fuel supply to an anode side and a cathode side of the fuel cell. The controller controls an oxidant supply to the anode and cathode sides to exothermically react with the hydrocarbon fuel when a temperature of the fuel cell is below a threshold temperature. When the temperature is greater than the threshold temperature, the controller terminates supply of the hydrocarbon fuel and the oxidant to the anode side. The controller terminates supply of the hydrocarbon fuel to the cathode side, and supplies a hydrogen-containing feed to the anode side.