Background: Agro-food supply chains possess specific characteristics due to the diverse nature of products involved and contribute to all three pillars of sustainability, making the optimal design of a sustainable agro-food supply chain a complex problem. Therefore, efficient models incorporating the unique characteristics of such chains are essential for making optimal supply chain decisions and achieving economically and environmentally sustainable agro-food supply chains that contribute to global food security. Methods: This article presents a multi-objective mixed-integer linear programing model that integrates agricultural-related strategic decisions into the tactical design of an agro-food supply chain. The model considers transportation, inventory, processing, demand fulfilment, and waste disposal decisions. It also accounts for seasonality and perishability, ensuring a comprehensive approach to sustainability. The model aims to maximize the total generated profits across the supply chain while simultaneously minimizing CO₂ emissions as a measure of environmental impact. Results: By implementing the model on a sugar beet supply chain in the Netherlands, strategic crop rotation farm schedules for the crop rotation cycle and the optimum supply network decisions are obtained. Furthermore, different objectives are analyzed and the Pareto-efficient frontier is investigated to analyze the underlying trade-offs. Additionally, the model serves as a decision support tool for managers facilitating informed investment decisions in technologies that prolong product shelf life while maintaining profitability. Conclusions: The proposed multi-objective model offers a valuable framework for designing economically and environmentally sustainable agro-food supply chains. By aligning with sustainability goals and providing decision support, this research contributes to enhancing global food security and promoting sustainable resource utilization.