The invention relates to fuel cell systems and associated methods of operation where an electrochemical cell such as a fuel cell is used as an electrochemical hydrogen separator to separate hydrogen from a process stream (e.g., reformate or synthesis gas), or as an electrochemical hydrogen expander to inject hydrogen into a process stream. In one aspect, the invention provides a method of operating a fuel cell system, including the following steps: flowing hydrogen from a hydrogen supply conduit through a fuel cell to provide an electric current to a load coupled to the fuel cell; actuating an electrochemical hydrogen separator in a first mode of operation of the system to transfer hydrogen from the hydrogen supply conduit to a hydrogen storage vessel; and actuating an electrochemical hydrogen expander in a second mode of operation of the system to transfer hydrogen from the hydrogen storage vessel to the fuel cell.