In this study, a novel three-compartmented electrochemical bioreactor (3-CEB) was designed in an effort to overcome the disadvantages of the two-compartmented electrochemical bioreactor (2-CEB) separated with a cation-selective membrane for enrichment of strict anaerobes. The 3-CEB was comprised of an anode, outlet, and a cathode compartment. The outlet compartment was positioned between the anode and cathode compartment, and it was separated with the anode side by a rubber plate and with the cathode side by a porous glass membrane. A platinum wire bridging the anode and outlet compartment operated as a redox passage, however, through which no material could permeate. Butyrate fermentation bacteria were enriched on the basis of the metabolite production. Butyrate generated by strict anaerobes was significantly more abundant in the 3-CEB than in the 2-CEB. Acetic acid and lactic acid generated by facultative anaerobes was relatively higher in the 2-CEB than in the 3-CEB. Meanwhile, butyrate was not generated in the bioreactor utilized for the control test, to which the electrochemical potential was not charged. In a continuous culture using the 3-CEB, the majority of the glucose was fermented to butyrate, and the acetate additionally supplied to the bacterial culture was metabolically reduced to butyrate. More lactate than butyrate was generated from glucose in the 2-CEB.