•A comprehensive mathematical model is proposed for biofuel supply chain design.•We link the three dimensions of sustainability using multiobjective programming.•Dynamic capacity strategy in facilities is addressed.•A realistic case study in Colombia is conducted. Biofuel production from agricultural waste has been identified as a promising strategy in the field of renewable energy. This topic involves complex mathematical modeling tasks such as feedstock characteristics, biorefinery location, capacity strategy and material flows. This paper proposes a Multiple Objective Mixed Integer Linear Programming model (MOMILP) for the design of a sustainable supply chain using multiple agricultural residues. The proposed comprehensive model is utilized in a case study in Colombia, using coffee crop residues. Computational results show the model’s robustness as a decision-making tool, which allows the projection of a flexible supply chain structure in the long term.