The control of a thermophilic continuous anaerobic digestion system when subjected to potential inhibitory shock loadings was achieved through the regulation of dissolved H2, monitored using membrane inlet mass spectrometry, by the controlled addition of carbon source. At a feed pump switching threshold equivalent to 1 μmol/1 H2a steady state rate of methanogenesis of approximately 40 μmol/1/min was obtained. Higher H2thresholds resulted in an inhibition of methanogenesis, but precise control of H2concentration was demonstrated with an oscillatory response of period 2·5–5·