Food supply chains significantly influence environmental sustainability and public health due to high energy use, emissions, and waste generation. Existing studies rarely integrate food supply chains with biofuel and bioenergy production, especially considering resource constraints and health outcomes. This paper addresses this gap by proposing a novel two-phase method for designing and optimizing a sustainable hybrid food-biofuel-bioenergy supply chain, incorporating the food-energy-water-health-pollution nexus. In the first phase, optimal locations for cultivating biomass resources (Jatropha and Microalgae) are determined using fuzzy methods within a Geographic Information System. The second phase develops a multi-objective mathematical optimization model that is solved by the Lp-metric method and validated through real-world data from Iran's food industry. The proposed network emphasizes sustainability through circular bio-economy practices, including wastewater recycling, food waste utilization, and replacing gasoil with biodiesel (20 % biodiesel, 80 % gasoil). Quantitative results demonstrate a 43 % reduction in greenhouse gas emissions, annual food products health improvements of 4 %, and efficient water resource management limiting increased water consumption to just 7 %. The network becomes profitable within seven years, with over 50 % of bioenergy derived from waste-based biomass. These innovations offer actionable insights for policymakers and managers pursuing integrated, sustainable solutions to enhance environmental performance, public health, and energy resilience.