The invention is an apparatus and method to remove hydrogen sulfide and siloxanes from biogas and destroy the contaminants in microwave reactors. Hydrogen sulfide and siloxane are removed from biogas using an adsorbent media such as activated carbon. The media is regenerated in a microwave reactor where the hydrogen sulfide and siloxane are removed in a sweep gas. In one process, siloxane is oxidized to silicon dioxide in a second microwave reactor and removed with a filter. Hydrogen sulfide if first oxidized to sulfur dioxide, then reduced to sulfur in a third microwave reactor and removed with a filter. In another process, siloxane is combined with water to form silicon dioxide and hydrogen sulfide is reduced to elemental sulfur in a microwave reactor. These reactants are removed with a filter. The remaining sweep gas containing hydrogen and low molecular weight hydrocarbons is returned to the biogas stream.