Granulated Activated Carbon (GAC) is used to remove hydrogen sulfide (H2S) from the biogas produced in an anaerobic digester. The cleaned biogas is then combusted in a reciprocating engine. The exhaust of the engine is passed through a heat exchanger and then through GAC in an adsorber to adsorb nitrogen oxides (NOx) and any sulfur oxides (SOx). The GACs containing NOx, H2S, and SOx, are transported to a microwave reactor, mixed, and exposed to microwave energy. The H2S and NOx are desorbed from the GAC and chemically combined to produce nitrogen, carbon dioxide, sulfur and water. Unreacted nitrogen oxides or hydrogen sulfide are transported to a second reactor containing carbon media to be reacted by a further microwave process. Sulfur is removed with a filter as a solid and the remaining inert components are vented to the atmosphere. The GAC is regenerated and reused to remove additional H2S and NOx.