Abstract: The present disclosure is directed to systems and methods for independently controlling the operation of fuel cell stacks and to fuel cell systems incorporating the same. These systems and methods may include providing a fuel cell system including a plurality of fuel cell stacks and at least a first energy storage device and controlling the operation of the plurality of fuel cell stacks based at least in part on a variable associated with the fuel cell system and/or an energy consuming device. These systems and methods may further include beginning production of electrical output from the fuel cell system responsive to a start condition, initiating production of electrical output from the plurality of fuel cell stacks responsive to a plurality of stack start conditions, and ceasing the production of electrical output from the fuel cell stacks responsive to at least a first stack stop condition.