Manual assembly systems are featured with high flexibility but with the risk of lower quality, higher cycle time, inefficient resource employment, and affecting sustainability goals in comparison to fully automated ones. Conventional automated assembly is challenged by the desired level of flexibility when compared to what automation through Plug & Produce system represents. Plug and Produce, during the last few decades aimed at addressing highly flexible automation systems handling rapid changes and adaptations as one dominant solution. Multi-agent System (MAS) as a tool to handle different areas of manufacturing control systems can be used in Plug & Produce representing every physical control entity (e.g., parts, resources) as agents. This article aims to describe a model-based configurable multi-agent design in Plug and Produce system together with a prototype implementation of the actual automated assembly use case of a kitting operation highlighting flexibility and reconfigurability and the model functionality. A model-based approach with a few models using UML standards describes the structure and behavior of the system. Model instantiation is introduced and followed by real prototype use case implementation. The use case study of advanced automated kitting operation in the assembly automation domain has been selected. Agent-based operation control systems have been applied during the assembly process. The evaluation was accomplished by testing several scenarios on Plug & Produce for kitting operation. To conclude, several desirable functionality features of the framework during the demonstration such as rapid instantiation and adaptation, and in particular, the flexibility features have been examined and evaluated with several failure-handling testing scenarios.