Today’s industry needs to be able to produce customized products in small batches with agility, low cost, and acceptable quality levels. The constant introduction of new products requires a rapid response to changes in the market and the implementation of innovative strategies. Manufacturing systems have evolved to meet market demands, considering crucial variables such as complexity, innovation, and responsiveness. Automation, using intelligent devices and various types of control, proposes models and solutions to make industrial operations more flexible. Petri Net modelling, a graphical technique that provides a clear and concise visual representation of complex systems, may intuitively map production line processes. Integrating world-class manufacturing (WCM) principles enhances the framework’s effectiveness. In this context, this article proposes a conceptual framework that combines reconfigurable manufacturing systems (RMS) concepts modelled by Petri Nets, the assignment of weights inspired by WCM, and simulation using the Digital Twin (DT). The framework offers a new horizon for achieving operational efficiency and continuous adaptation. Using simulation in a virtual environment it took a proactive approach to validate the framework’s effectiveness. This crucial step makes it possible to compare the results obtained virtually with the actual processes on the production lines. Applying this simulation verifies the model’s robustness and provides crucial insights for ongoing adjustments.