An ion source assembly and method has a source gas supply to provide a molecular carbon source gas to an ion source chamber. A source gas flow controller controls flow of the molecular carbon source gas to the ion source chamber. An excitation source excites the molecular carbon source gas to form carbon ions and radicals. An extraction electrode extracts the carbon ions from the ion source chamber, forming an ion beam. An oxidizing co-gas supply provides oxidizing co-gas to chamber. An oxidizing co-gas flow controller controls flow of the oxidizing co-gas to the chamber. The oxidizing co-gas decomposes and reacts with carbonaceous residues and atomic carbon forming carbon monoxide and carbon dioxide within the ion source chamber. A vacuum pump system removes the carbon monoxide and carbon dioxide, where deposition of atomic carbon within the ion source chamber is reduced and a lifetime of the ion source is increased.