Biofuel production includes several partial processes. Many recent studies deal with thermochemical and enzymatic pre-treatment of lignocellulose, ethanol and biogas generation as well as utilization of residual products from ethanol fermentation in a biorefinery approach. However, an essential process like conservation of biomass is poorly investigated, although it consumes a considerable proportion of total input energy. Within the MicroDrive-programme we are investigating key issues of biofuel production, including storage of biomass, thermochemical and enzymatic pre-treatment, bioethanol and biogas production, utilization of fermentation residues for feed, and biogas production remnants as fertilizers. We found for instance that an alternative storage method can substantially improve total energy output of ethanol production. When ethanol and biogas were produced from lignocellulose the total energy output was increased. In such integrated approach ethanol production from sugars usually not fermented by the yeast is not critical for the efficiency of the whole process because biogas is generated from these sugars in a later stage. However, ethanol processes where sugars are not utilized are prone to bacterial infections, presenting a special request for robust yeast strains, which we are investigating within the programme. Moreover, for optimized bioethanol/biogas production it is also necessary to adapt the pre-treatment method, avoiding the release of inhibitors and sulphate, which can disturb the biogas process. Fermentation remnants are energy rich substrates for biogas production, but specific microbial biogas consortia are required that can cope with the high ammonium content in the biogas process. Those consortia are also studied within MicroDrive.