Reformate hydrogen from biogas is an attractive fuel alternative for energy conversion in PEM fuel cells. However, in the reformate traces of ammonia may be found, e.g. if the biogas is produced from agricultural resources. In this investigation the effect of ammonia in the fuel gas, on each part of the fuel cell, is studied by cyclic voltammetry, electrochemical impedance spectroscopy (EIS), symmetrical hydrogen cell (H-2|H-2)- and real fuel cell operation. A considerable degradation in performance is observed by introducing 200 ppm ammonia. The results show that ammonia not only affects the polymer electrolyte membrane but also the oxygen reduction reaction (ORR) and catalyst ionomer in both electrodes, whereas the hydrogen oxidation reaction (HOR) is the worst affected. In the short-term, the performance is reversible if running the cell on neat hydrogen after ammonia exposure, but this does not apply for long-term exposure. A mitigation method with air bleed is tested but gives no improvement of the performance. (C) The Author(s) 2018. Published by ECS. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives 4.0 License.