Improving biofuel yield and water reuse are two important issues in the further development of biorefineries. 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 biorefinery 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 significantly 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 efficiency and ability to recycle water. Conversion of the sugar- and lignin-degradation products to hydrogen is synergistic with biorefinery 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 biorefineries capable of improving energy efficiency by up to 30% are discussed. Published in 2011 by John Wiley & Sons, Ltd