Reduced sulfur compounds emitted from livestock production cause odor nuisance for local residents. The microbial processes responsible for this are not well described in swine manure and a method for monitoring the biological processes is necessary to develop strategic abatement technologies. In this study, Proton-Transfer-Reaction Mass Spectrometry and isotope-labeled sulfate were combined and applied to elucidate the sulfur processes in swine manure with high time resolution. We successfully monitored reduction of isotope 33S labeled sulfate into corresponding 33S hydrogen sulfide and found that some of the 33S hydrogen sulfide was further methylated into 33S methanethiol. The isotope patterns in reduced sulfur compounds together with usage of inhibitors enabled us to calculate a sulfate reduction rate of 1.03 ± 0.18 mM/day equivalent to 76.9 ± 3.0% of total hydrogen sulfide emissions. Cysteine degradation constituted 20.2 ± 2.7% of the total hydrogen sulfide produced and the remaining hydrogen sulfide came from demethylation of methanethiol and dimethyl sulfide. Another source to methanethiol, besides hydrogen sulfide methylation, was methionine degradation, which contributed with 78.3 ± 2.5% of the methanethiol production, whereas the remaining 21.7 ± 2.5% came from hydrogen sulfide methylation. This study suggests, therefore, that emissions of odorous sulfur compounds from swine manure can be reduced by inhibiting methionine degradation and sulfate reduction.