This paper develops a mixed-integer linear programming (MILP) formulation to support the design and planning of agri-food supply chains (AFSC). The model focuses on the strategic-tactical decisions of capacity definition, selection of processing technologies, and the establishment of product flows to achieve expected net present value (ENPV) maximisation. Within the model, AFSC-specific characteristics are modelled as is the case of product perishability, flexible storage strategies, and reverse logistics operations. Supply and demand uncertainty is considered using a stochastic scenarios tree. The model is tested via the application of a case study from an existing sugar beet processing supply chain in The Netherlands.