Hydrogen is an alternative energy source that can replace fossil fuels. The latest breakthrough idea for producing hydrogen fuel is by utilizing biomass in bioelectrochemical systems, which is Microbial Electrolysis Cell (MEC). MEC is a method for producing hydrogen gas that is managed from organic materials, including from wastewater. In addition to very low energy consumption, the MEC system is able to use sludge waste as a substrate for the bacterial community to be implemented. The rate of hydrogen production with MEC is relatively lower when compared to air fermentation and electrolysis methods. Efforts that can be made to increase hydrogen production are by operating the MEC system at optimal distance between electrodes. One of the major problems that arises from the use of the MEC system is methanogens, the methane-producing bacteria. This methanogen consumes biohydrogen produced at the cathode which cause the loses of biohydrogen production in MEC system. In this research, biological control methods is utilized in bioelectrode by enriching it with denitrifier bacteria to inhibit the growth of methanogens. The MEC reactor is carried out in configuring a single-chamber MEC. Variation in denitrifier bacteria used and distance between electrodes aim to find the optimal conditions. The composition of the reactor chamber gas head is supported by using Gas Chromatography to analyze hydrogen and methane reserves. The addition of Pseudomonas stutzeri as biological control of methanogenesis could reduce the methane up to 76.28% compared to the control reactor at the first cycle. The presence of Pseudomonas stutzeri was also able to increase the H2 produced 128% higher compared to the control reactor. With the electrode spacing 0.5 cm, the H2 produced 65% was higher than the MEC reactor with 1 cm-electrode spacing. The 0.5 cm space was the optimum space for this experiment since it still supported the growth of the exoelectrogen bacteria and reduced the internal resistance within the MEC system.