Sulfur compounds poison catalysts, such as the anode catalysts and reformer catalysts within molten carbonate fuel cell systems. This poisoning is eliminated using a sulfur scrubber 29 located prior to the inlet of the cathode chamber 13. Anode exhaust 19 which contains water, carbon dioxide and possibly sulfur impurities, is combined with a cathode exhaust recycle stream 22 and an oxidant stream 25 and burned in a burner 33 to produce water, carbon dioxide. If sulfur compounds are present in either the anode exhaust, cathode exhaust stream, or oxidant stream, sulfur trioxide and sulfur dioxide are produced. The combined oxidant-combustion stream 27 from the burner 33 is then directed through a sulfur scrubber 29 prior to entering the cathode chamber 13. The sulfur scrubber 29 absorbs sulfur compounds from the combined oxidant-combustion stream 27. Removal of the sulfur compounds at this point prevents concentration of the sulfur in the molten carbonate fuel cell system. Therefore, neither the reformer catalysts nor the anode 17 experience sulfur poisoning.