Manufacturing Execution System (MES) has been applied to plan and manage production on the shop floor level. Some of its functions include monitoring output, quality control data, and operator productivity. It works between the automation layer and the administrative IT systems, enabling the vertical integration of information. Although MES has already been applied in manufacturing for many years, we argue that the MES is well-developed to play a central role in Industry 4.0 implementation efforts. Advanced connectivity has allowed the MES to gain more information from the shop floor entities. In this scenario, MES may be an integration backbone for Industry 4.0, connecting machines to the manufacturing control logic, collecting data, and providing information for decision making. This paper aims to discuss an updated view of MES’s role in manufacturing as a fundamental enabler for data integration in Industry 4.0 environments. A pilot advanced MES case application in an Industry 4.0 manufacturing environment is developed and described. A learning factory has been selected for the pilot application in this research due to its flexibility to allow the necessary IT system changes. In the developed scenario, an MES is applied to control the manufacturing of a customized product. The MES receives the product configuration data from the ERP system, controls shop floor equipment, and manages operators’ activities. Product data is gathered along the process. Based on this case application, current MES potential and limitations are explored.