In this paper, we presented a novel microbial fuel cell (bMFC) structure, with a bipolar membrane separating the anode and cathode chambers. A bipolar membrane divides the bMFC into anode and cathode chambers. The bipolar membrane comprises anion and cation exchange layers. The anode chamber side has the cation exchange layer, while the cathode chamber side has the anion exchange layer. The anode chamber of the bMFC was loaded with Shewanella oneidensis MR-1 and lactic acid, while the cathode chamber was loaded with pure water and iron (III) hydroxide. The bMFC generated electrons for 20 days at a maximum current density of 30 mA/m2 and the ohmic resistance value was estimated to be 500 Ω. During the operation of the bMFC, both the anode and cathode chambers kept anaerobic conditions. There was no platinum catalyst in the cathode chamber, which is required for the reaction of protons with oxygen. Therefore, oxygen could not serve as an electron acceptor in the bMFC. We considered a bMFC mechanism in which protons produced by S. oneidensis react with hydroxide ions, the counter anions of Fe3+, inside the bipolar membrane to produce water. In other words, the electron acceptor in bMFC would be Fe3+.