This paper reports a thermodynamic-based study into the production of hydrogen via biogas decomposition for use in polymer electrolyte membrane fuel cells (PEMFC) and solid oxide fuel cells (SOFC). For biogas with a CO2/CH4 ratio of 40 : 60, it was necessary to separate carbon dioxide before supplying the biogas to the decomposition unit to achieve higher performance. However, the decomposition of biogas with CO2 capture under autothermal conditions was not compatible with PEMFCs because the CO concentration was higher than 10 mu mol/mol. For application in SOFCs, the highest H-2 yields were achieved by combusting the methane-rich gas split from the decomposition reactor feed stream to heat the system, while those obtained by combusting the gas split from the decomposition reactor product stream resulted in the highest carbon yields and lowest overall CO2 emissions.