Removal of volatile fatty acids in anaerobic digestion of organic wastes can accelerate eventual decomposition of organic wastes to CO2 and H2O using a recovery of electric energy by a microbial fuel cell. The fuel cell anode chamber was a 10 cm (I.D.)×20 cm long cylindrical Plexiglass having an ion ceramic cylinder separator (I.D.10 mm, O.D.12 mm, 0.3 μm average pore size). The aluminum foil cathode (12 cm2 surface area) was located inside the ceramic cylinder. Between the two cylinders, 1 liter of activated carbon particles was packed as anode electrode having a void fraction of 0.4. This fuel cell was connected to a 5 liter bioreactor (working volume 1.5 liter), and the bioreactor was run in batch mode by re-circulating a synthetic wastewater of 5 g/L glucose. Maximum TVFA (total volatile fatty acids) and SCOD (soluble chemical oxygen demand) removal rate were 3.79 g/L·day, 5.88 g/L·day, respectively. TVFA removal efficiency (92.7%) and SCOD removal efficiency (94.7%) under maximum current density operation were higher than the operation with maximum power density. In acid fermentation, butyric acid concentration was highest because Clostridium butyricum was a dominant microbial communitiy in the inoculum. The microbial cells collected from the anode bio-film samples were affiliated with Bacillus cereus based on the nucleotide sequences of dominant DGGE (denaturing gradient gel electrophoresis) bands.