A method for start-up and shut down of a fuel processor including an autothermal reformer employing a non-pyrophoric shift catalyst is disclosed. Also disclosed are a computer programmed to start-up or shut down a fuel processor including an autothermal reformer employing a non-pyrophoric shift catalyst or a program storage medium encoded with instruction that, when executed by a computer, start-up or shut down a fuel processor including an autothermal reformer employing a non-pyrophoric shift catalyst.