Abstract This work presents a mathematical model for the strategic planning of the energy supply chain accounting for fossil fuels and biofuels. The proposed model considers the fuel extraction, production, processing, and distribution to the consumer, as well as the interaction with forest plantations to capture emissions generated in the whole process. Matching law is incorporated to predict, control and understand the situation under study. People's behavior has been included to determine their preference for deciding whether to install a refinery or a biorefinery. The decision is influenced by economic factors such as emissions taxation. The proposed approach was applied to a case study in Mexico, where the profit of the whole system, generated emissions, and jobs are considered. Results show that by implementing matching law it is possible to promote biofuels production together with fossil fuels, as well as to determine the preferences in the system.