A fuel cell system is disclosed, which includes an anode recirculation loop comprising a fuel cell stack for generating power, a flowmeter for measuring a fuel flow rate of a fuel provided into the anode recirculation loop, a current measuring device for measuring a current drawn from the fuel cell stack, a recycle ratio measuring device for measuring a recycle ratio in the anode recirculation loop, and a processor for estimating a fuel utilization of the fuel cell stack based on the measured fuel flow rate, the measured current and the measured recycle ratio. Methods for operating the fuel cell system are also disclosed.