The Manufacturing Execution System (MES) is a process-oriented IT solution collecting and managing information from the shop floor manufacturing processes. Because of the programming and customization effort required for specific production processes, the MES implementation is not widespread in the food and beverage industry, as most food and beverage manufacturers are small- and medium-sized enterprises with limited resources to invest in MES. For engineering the MES that should be customized according to the target production processes, a model-driven approach has been presented in this paper with six phases covering the entire lifecycle of the MES engineering process. By using this approach, MES can be automatically generated and sustainably improved, which has the potential to reduce the complexity of implementation as well as the resources required for the engineering of customizable MES. Based on two use cases in the processing and packaging areas in the food and beverage industry, the feasibility and practicality of the presented approach have been proven.