<p>Renewable energy sources have become increasingly appealing due to the major environmental issues and depletion of fossil fuels. Bioenergy production from first/second/third-generation biomass is one of the more promising renewable energy sources that do not jeopardize food safety. The design of the biomass-to-bioenergy supply chain indicates a complex challenge that has garnered significant interest from both academic and industrial research. To produce sustainable energy in all types of climates and geographical areas, even isolated ones, three distinct categories of biomass that are sunflower seeds, waste animal fat, and microalgae are being jointly examined as feedstock. A multi-objective framework is established to construct the supply chain for first, second, and third-generation biofuels. The proposed model focuses on key decisions such as the selection of raw material resources, the placement of production facilities, the positioning of warehouses, and the optimization of material flow to effectively reduce total costs while enhancing energy output. The evaluation and validation of this model are conducted through the implementation of the genetic algorithm. The validation of the solution method and framework is conducted through numerical illustrations. The analysis indicates that the preliminary expenditures for a biodiesel production facility constitute 57% of the overall costs, underscoring the substantial installation expenses associated with the supply chain. Their contribution accounts for 65% of the total environmental installation impact. A sensitivity analysis is performed to evaluate the feasibility of this study. The proposed framework presents potential benefits for traders and regulatory bodies involved in the biofuel sector.</p>