This study evaluated performance of an upflow membraneless microbial electrolysis cell (MEC) with flow-through electrodes for wastewater treatment. First, methane production and COD removal were evaluated in continuous flow experiments carried out using synthetic and municipal wastewater. A 29–75% increase in methane production was observed under bioelectrochemical conditions as compared to an anaerobic control. Next, simultaneous removal of COD and nitrogen was studied under microaerobic conditions created by continuous air injection to the anodic compartment of the MEC. While the presence of oxygen decreased Coulombic efficiency due to aerobic degradation of COD, enhanced ammonium removal with near zero nitrite and nitrate effluent concentrations was observed. Evidence of direct ammonium oxidation at the anode as well as nitrite and nitrate reduction at the cathode was obtained by comparing performances of MECs operated under anaerobic and microaerobic conditions with the control reactor operated at zero applied voltage.