A unique method was developed and applied for monitoring methanogenesis pathways based on isotope labeled substrates combined with online membrane inlet quadrupole mass spectrometry (MIMS). In our study, a fermentation sample from a full-scale biogas plant fed with pig and cattle manure, maize silage, and deep litter was incubated with 100 mM of [2-(13)C] sodium acetate under thermophilic anaerobic conditions. MIMS was used to measure the isotopic distribution of dissolved CO2 and CH4 during the degradation of acetate, while excluding interference from water by applying a cold trap. After 6 days of incubation, the proportion of methane derived from reduction of CO2 had increased significantly and reached up to 87% of total methane, suggesting that synthrophic acetate oxidation coupled to hydrogenotrophic methanogenesis (SAO-HM) played an important role in the degradation of acetate. This study provided a new approach for online quantification of the relative contribution of methanogenesis pathways to methane production with a time resolution shorter than one minute. The observed contribution of SAO-HM to methane production under the tested conditions challenges the current widely accepted anaerobic digestion model (ADM1), which strongly emphasizes the importance of the acetoclastic methanogenesis.