The transition towards more sustainable biofuels systems might be conveniently driven by purpose-devised quantitative decision-making tools based upon the optimisation of the entire Supply Chain (SC). In this work, a moMILP (multi-objective Mixed Integer Liner Programming) modelling framework is proposed to support strategic investments on bioethanol infrastructures considering both economic and environmental sustainability (e.g., impact on global warming and water resource). Corn grain and stover are accounted for as feedstocks for ethanol production; Northern Italy is taken as a geographical reference. Results show that investments strategies are affected by the trade-off between environmental and financial objectives.