Global warming, adverse environmental consequences, and the rapid depletion of oil resources are some of the critical challenges that humanity presently confronts due to the utilization of fossil fuels. Replacing fossil fuels with renewable sources of energy such as biofuel is crucial for a clean environment. In addition to its numerous advantages, the production of biofuels has detrimental effects on natural resources as well. Water, energy, food, and land are all required to produce food and energy, which are inextricably linked as the essential inputs for agriculture and fuel production. Undesirable climate change and its impacts on ecosystems are also consequences of this process. This study offers a two-phase approach to designing a canola-to-biodiesel supply chain. The first phase is concerned with finding appropriate sites for canola cultivation in accordance with climatic, social, economic and design criteria. To achieve an ideal solution, the fuzzy best-worst method andthe fuzzy technique of order preference similarity to the ideal solution are simultaneously used. In the second phase, a new multi-objective integer programming model that involves a water-energy-food-land-ecosystem-undesirable climate change nexus is introduced. The suggested model enhances crop harvest from desirable agricultural areas, maximizes the profit, preserves ecosystem values, mitigates undesirable climate changes, and reduces water and energy consumption. An interactive fuzzy method is used to solve the model, and the efficiency of the proposed model is evaluated through a real case study for Iran. Sensitivity analyses are also performed on the key parameters. According to the findings, production activities are connected with the increase of network costs, adverse changes in climate, and increased use of energy. Thus, using high-yield catalysts, increasing the production scale, complying with environmental regulations, receiving government subsidies, investing in research to improve production technologies, and identifying cost-saving strategies can minimize harmful environmental effects and reduce biodiesel production costs, thereby boosting the profit. Furthermore, given Iran’s water scarcity and reduced rainfall, increasing the canola yield per hectare might lead to less land use and water consumption for irrigation. Utilizing specialized machinery, enhancing farmers’ skills in canola cultivation, supplying seeds on time, planting promptly, providing optimal nutrition, and promoting pest management are all effective methods to boost canola yields. The insights provided in this study can help managers in the canola-based biodiesel production sector make better decisions.