A mathematical model for the semi-batch operation of tray tunnels for food deep chilling is presented and analyzed. Design aspects are discussed involving both single tunnels and systems of parallel tunnels. In both cases, optimum flowsheet configuration and operating conditions are sought and verified by appropriate formulation of design and optimization strategies. The optimization objective is the total annual cost of the plant, subject to constraints imposed by the operation of the chilling tunnel, thermodynamics and construction. The decision variables were the number of trucks, the operating temperature and flowrate of the cooling air stream, the refrigeration cycle heat exchanger temperature, as well as the total number of sections involved. The Mixed-Integer Non-Linear Programming (MINLP) nature of the design problem required mathematical programming techniques for its solution. The optimization was carried out for a wide range of production capacities, and the optimal points, where a new truck or a new section is introduced, were evaluated. The analysis focused on the design of tray tunnels for the most popular food product treated by deep chilling meat slabs. A characteristic case study is presented in order to demonstrate the effectiveness of the proposed approach.