A flue gas desulfurization process and system that utilize ammonia as a reactant, and in which any hydrogen sulfide and/or mercaptans within the ammonia are separated during the desulfurization process so as to prevent their release into the atmosphere. The process and system entail absorbing acidic gases from a flue gas with a scrubbing media containing ammonium sulfate to produce a stream of scrubbed flue gas, collecting the scrubbing media containing the absorbed acidic gases, injecting into the collected scrubbing media a source of ammonia that is laden with hydrogen sulfide and/or mercaptans so that the injected ammonia is absorbed into and reacted with the collected scrubbing media, stripping the hydrogen sulfide and/or mercaptans from the collected scrubbing media by causing the hydrogen sulfide and/or mercaptans to exit the collected scrubbing media as stripped gases, and collecting the stripped gases without allowing the stripped gases to enter the stream of scrubbed flue gas.