Improving biofuel yield and water reuse are two important issues in the further development of biorefi neries. An alternative to the typical combustion-based approach to handle residual organics stream by implementation of bioelectrochemical systems such as microbial fuel cells (MFCs) and/or microbial electrolysis cells (MECs) to improve energy recovery from biomass is presented. The potential advantages of this alternative scheme in a biorefi nery include minimization of heat loss and generation of a higher-value product: electricity (in MFC) or hydrogen (MEC). The need for 5-15 gallons of water per gallon of ethanol can be reduced signifi cantly via recycling of water after MEC treatment. Removal of inhibitory byproducts such as furans, phenolics, and acetate in MFC/ MECs to generate energy, thus, has dual advantages: improvements in energy effi ciency and ability to recycle water. Conversion of the sugar-and lignin-degradation products to hydrogen is synergistic with biorefi nery hydrogen requirements for upgrading Fischer-Tropsch (F-T) liquids and other byproducts to high-octane fuels and/or high-value products. Some of these products include sorbitol, succinic acid, furan and levulinate derivatives, glycols, polyols, 1,4-butenadiol, phenolics polymers, etc. Potential process alternatives utilizing MECs in biorefi neries capable of improving energy effi ciency by up to 30% are discussed. Published in