We are using a PEM system to demonstrate bio-oil upgrading at mild conditions. Bio-oil is a mixture of hundreds of inorganic and organic compounds with an aqueous and non-aqueous phase. It contains reactive, acidic and oxygenated species which cause condensation and polymerization reactions. It is long believed that active groups such as phenolics and carbonyls are responsible for these reactions. Therefore, prior to use as a transportation fuel, the oils need to be stabilized (upgraded) to hydrogenate unstable and/or corrosive species. Conventional bio-oil hydrogenation occurs at moderate temperatures (300°C) and hydrogen pressures up to 2000psi. We have modified a PEM fuel cell to perform bio-oil hydrogenation to stabilize the more reactive compounds using protons and water as the hydrogen source at room temperature. Electrochemical hydrogen generation is a common competing reaction. This eliminates the high temperature and externally supplied high pressure hydrogen which may decrease the cost of bio-fuels and products. By modifying the PEM cell structure and electrode materials promising results have been observed where significant hydrogenation was found. The novel cell structures and electrode materials resulted in improved current efficiencies for electrochemical reduction of organic species. A description of work conducted and a discussion of results will be presented.