•Trends in Industry 4.0 (I4.0) are influencing the development of manufacturing execution systems.•I4.0-related requirements of MES functionalities are determined.•MESs should interconnect all components of cyber-physical systems.•Formal models and ontologies will play essential role in I4.0 systems.•The overview can serve as a guide for engineers as well as for researchers. This work presents how recent trends in Industry 4.0 (I4.0) solutions are influencing the development of manufacturing execution systems (MESs) and analyzes what kinds of trends will determine the development of the next generation of these technologies. This systematic and thematic review provides a detailed analysis of I4.0-related requirements in terms of MES functionalities and an overview of MES development methods and standards because these three aspects are essential in developing MESs. The analysis highlights that MESs should interconnect all components of cyber-physical systems in a seamless, secure, and trustworthy manner to enable high-level automated smart solutions and that semantic metadata can provide contextual information to support interoperability and modular development. The observed trends show that formal models and ontologies will play an even more essential role in I4.0 systems as interoperability becomes more of a focus and that the new generation of linkable data sources should be based on semantically enriched information. The presented overview can serve as a guide for engineers interested in the development of MESs as well as for researchers interested in finding worthwhile areas of research.