Large scale transformation of biomass to more versatile energy carriers has most commonly been focused on one product such as ethanol or methane. Due to the nature of the biomass and thermodynamic and biological constraints, this approach is not optimal if the energy content of the biomass is supposed to be exploited maximally. In natural ecosystems, biomass is degraded to numerous intermediary compounds, and we suggest that this principle is utilized in biorefinery concepts, which could provide different fuels with different end use possibilities. In this chapter we describe one of the first pilot-scale biorefineries for multiple fuel production and also discuss perspectives for further enhancement of biofuel yields from biomass. The major fuels produced in this refinery are ethanol, hydrogen, and methane. We also discuss the applicability of our biorefinery concept as a bolt-on plant on conventional corn- or grain-based bioethanol plants, and suggest that petroleum-base refineries and biorefineries appropriately can be coupled during the transition period from a fossil fuel to a renewable fuel economy.