Fuel cell systems and associated methods of operation are provided whereby application of a fuel cell is coordinated with a fuel processor and a hydrogen separator. One such method includes the following steps: (1) operating a fuel processor to convert a hydrocarbon to reformate; (2) reacting the reformate in a fuel cell to generate electrical power; (3) supplying the electrical power to an electrical load, wherein the electrical load has a power requirement threshold; (4) determining whether the electrical power from the fuel cell is below the power requirement threshold; (5) increasing a flow of reformate from the fuel processor to the fuel cell when the electrical power from the fuel cell is below the power requirement threshold; (6) flowing a portion of the reformate from the fuel processor to a hydrogen separator; (7) storing hydrogen from the hydrogen separator in a hydrogen storage vessel; (8) monitoring an amount of hydrogen stored in the hydrogen storage vessel; and (9) adjusting a proportional valve upstream from the fuel cell toward a closed position when the amount of hydrogen in the hydrogen storage tank is below a predetermined threshold to increase a proportion of the reformate from the fuel processor that is flowed to the hydrogen separator.