Processes to shut down a fuel cell system are described. In one implementation (300), a load (215) is cyclically engaged and disengaged across a fuel cell stack (205) so as to deplete the fuel available to the system's fuel cells (205). Voltage and/or current thresholds may be used to determine when to engage and disengage the load (215) and when to terminate the shutdown operation. In another implementation (500), a variable load (405) is engaged and adjusted so as to deplete the fuel available to the system's fuel cells (205). As before, voltage and/or current thresholds may be used to determine when to adjust the load (405) and when to terminate the shutdown process. In still another implementation, a load (215 or 405) may be periodically engaged and disengaged during some portion of the shutdown process and engaged but adjusted during other portions of the shutdown process.