A fuel cell based power supply comprises a main power converter and control that allows the fuel cell stack to be electrically shorted from time-to-time to improve performance. Additionally, the power converter may temporarily disconnect the fuel cell stack from the load after shorting, allowing the fuel cell stack to return to an open circuit voltage, and/or provide current limiting during a period after shorting to provide stable operation while the fuel cell stack powers the load and recharges a power storage device.