The present invention provides methods and systems for producing biofuel and bioenergy products using, as starting raw material, xenobiotic materials or compounds. The xenobiotic materials or compounds may originate from industrial or chemical plants, municipal waste, pharmaceutical products, cosmetic and personal care products, or other sources, and may include aliphatic and aromatic hydrocarbons, chlorinated organic solvents and other halogenated hydrocarbons, as well as heteroaromatic compounds. In accordance with the invention, these materials act as a carbon source to support the metabolism of xenobiotic-degrading microorganisms, thereby producing biomass and/or biogas that may be converted to bioenergy products by microbial synthesis. For example, the biomass may be converted to products such as ethanol, methanol, butanol, and methane, among others. The biogas may be converted to hydrogen gas and biodiesel, among others. Thus, the present invention couples the microbial breakdown (decomposition) of xenobiotic materials with the microbial synthesis of biofuel, thereby supplying needed (inexpensive) energy products, while reducing environmental pollution and contamination, and reducing the costs associated with disposal of hazardous waste.