Hydrogen and methane were simultaneously produced in a two-phase reactor, operated to separate the reactions of hydrogen and methanogen production. Each reactor was inoculated with a seed enriched with different microbial consortia. The first phase was operated with a hydraulic retention time of 7 days and at an organic loading rate of 7.7 g VS L−1 d−1 that produced a stable pH of 5.5. This suppressed the growth of methanogens and as a result, the off gas contained up to 27% hydrogen. The second phase was operated with a hydraulic retention time of 12 days and at an organic loading rate of 3.6 g VS L−1 d−1. This permitted the growth of hydrogenotrophs and methanogens to produce methane at a concentration of 60%. Examination of the microbial population of the two reactors both microscopically and using PCR, showed an effective separation of hydrogen- and methane-producing microbial communities. The study revealed that the suppression of hydrogentrophs and methanogens can be achieved by adopting rapid method that leads the growth of hydrogen- and methane-producing granules in phase-separated anaerobic environment.