Vulnerability of water resources to nutrients led to progressively stricter standards for wastewater effluents. Modification of the conventional procedures to meet the new standards is inevitable. New technologies should give a priority to nitrogen removal. In this paper, ammonium chloride and urine as nitrogen sources were used to investigate the capacity of a microbial electrolysis cell (MEC) configured by cation exchange membrane (CEM) for electrochemical removal of nitrogen over open-and closed-circuit potentials (OCP and CCP) during biodegradation of organic matter. Results obtained from this study indicated that CEM was permeable to both organic and ammonium nitrogen over OCP. Power substantially mediated ammonium migration from anodic wastewater to the cathode, as well. With a urine rich wastewater in the anode, the maximum rate of ammonium intake into the cathode varied from 34.2 to 40.6 mg/L.h over CCP compared to 10.5-14.9 mg/L.h over OCP. Ammonium separation over CCP was directly related to current. For 1.46-2.12 mmol electron produced, 20.5-29.7 mg-N ammonium was removed. Current also increased cathodic pH up to 12, a desirable pH for changing ammonium ion to ammonia gas. Results emphasized the potential for MEC in control of ammonium through ammonium separation and ammonia volatilization provided that membrane characteristic is considered in their development.