There is described a method for managing a fuel cell system having a fuel contaminator present in an anode reactant, the method comprising: monitoring a fuel contaminator concentration in the anode reactant of a fuel cell stack, the fuel cell stack having a plurality of individual fuel cell units each having a membrane electrode assembly (MEA); detecting an increase in the fuel contaminator concentration in the anode reactant; and increasing, when the increase in fuel contaminator concentration is detected, a concentration of a compound that chemically reacts with the fuel contaminator in the anode reactant by a mass transfer through a membrane in the fuel cell system to reduce the fuel contaminator concentration.