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Food supply chains (FSCs) are one of the major sectors in the global economy. Developing efficient and cost-effective food supply chains, provide an opportunity for supply chain and logistics companies to survive in the increasingly competitive market of today. In order to achieve this, one of the methods is to enhance the traceability of food during production, transportation and storage throughout the entire supply chain network in order to improve and maintain the quality and safety of the food provided to customers. Other methods include design and optimization of a supply chain network towards objectives such as the minimization of costs, transportation time and environmental pollution, and the maximization of service level and profits and so on. This study proposes a radio frequency identification (RFID)-enabled monitoring system for a meat production and supply chains network that ensures the integrity and quality of its meat products. The study also includes the development of three multi-objective optimization models as an aid to solving the facility location and allocation problem and the quantity flow of products travelling throughout the meat supply chain network with respect to trade-off solutions among a number of objectives. To deal with the uncertainty of the input data (e.g., costs, capacity and demands), stochastic programming and fuzzy programming models were also developed. Furthermore, by applying suitable solution approaches, Pareto solutions can be obtained based on the developed multi-objective models. For this a decision-making algorithm was used to select the best Pareto solution. In order to examine feasibility and applicability of the developed approaches, a proposed RFID-enabled automated warehousing system and a proposed RFID-enabled passport tracking system were also used as case studies by applying the developed approaches for the design and optimization of these two systems, respectively. Research findings demonstrate that the proposed RFID-enabled monitoring system for the meat supply chain is economically feasible as a relatively higher profit can be achieved. The study concludes that the developed mathematical models and optimization approaches can be a useful decision-maker for tackling a number of design and optimization problems for RFID-based supply chains and logistics systems and tracking systems.