Abstract In the upcoming decade, biofuels made from agricultural residues, wastes and by-products will most likely present an integral part of biofuel provision to achieve greenhouse gas (GHG) reduction targets. This study provides an evaluation of potential changes in GHG emissions arising from the introduction of alternative fuels. To this end, potential changes in GHG emissions arising from the introduction of 36 biorefinery configurations in 26 EU member states providing a broad spectrum of products (e.g. biofuels, chemicals, feed and food additives) are assessed. Additional electrofuel production using biogenic CO2 is evaluated. The assessment considers country specific energy supply, market conditions and soil characteristics. The potential changes in GHG emissions arising from the introduction of these facilities range from −206 to 135 and from −221 to −17 g CO2 per MJ of bioethanol provided from wheat grains and wheat straw, respectively. The analysis reveals a high variability in GHG intensities related to marginal feedstock and energy supply as well as potentially occurring displacement effects depending on location. A Monte Carlo simulation confirms potential reductions in GHG emissions. Furthermore, the analysis shows that the methodology used within the EU to evaluate GHG emissions provided by the Renewable Energy Directive (II) denies market access to certain types of biorefineries and production modalities that bear the potential to reduce GHG emissions. It is concluded that EU biofuel policy strategies targeting (advanced) biofuels should consider local conditions and markets and should especially pay attention to potential changes in other markets.