A fuel cell system comprises a fuel cell including an anode and cathode, a fuel reformer, and a water gas shift reactor. The fuel cell system is shutdown by shutting down electrical generation and then supplying air to the water gas shift reactor to oxidize CO and H.sub.2 remaining in the water gas shift reactor after shutdown of electrical generation. The introduction of air to the water gas shift reactor controls CO poisoning of the fuel cell and the emission of flammable and poisonous gases from the fuel cell system after the shutdown of electrical generation.