One method of operating a fuel cell system including splitting a cathode exhaust from one or more fuel cell stacks in the system into a majority cathode exhaust stream comprising more than 50% of the cathode exhaust and a first cathode exhaust bypass stream, providing the majority cathode exhaust stream to an inlet of an anode tail gas oxidizer (ATO) containing a catalyst and providing the first cathode bypass stream downstream of the catalyst such that it bypasses the catalyst. Another method includes providing an air inlet stream to the SOFC system via a main air inlet, providing the air inlet stream from the main air inlet to a cathode recuperator, and providing a cooling medium to a heat exchanger to cool the cathode recuperator.