The invention is a reformate fuel treatment system for a fuel cell power plant that includes at least one fuel cell for generating electricity from process oxidant and reducing fluid reactant streams; fuel processing components including a steam supply and a reformer for producing a hydrogen enriched reformate fuel for the fuel cell from a hydrocarbon fuel; and, an ammonia removal apparatus that treats the reformate fuel to make it appropriate for supplying hydrogen to an anode electrode of the fuel cell. The ammonia removal apparatus may be a disposable ammonia scrubber, an ammonia scrubbing cool water bed and an ammonia stripping warm water bed, a pair of first and second regenerable scrubbers, or a single regenerable ammonia scrubber.