Industry 5.0 changes the paradigm of the current production model, with repercussions throughout the value chain, and opens up opportunities for new approaches that include reducing waste to optimize the use of the planet’s resources. This paper proposes a functional and executable model that implements a Holonic Manufacturing System (HMS) architecture inspired by the I5.0 guidelines. This architecture presents the factory floor as a service provider for the product to be built, intending to make the manufacturing process adaptable to changes. The model uses Reference nets as the modeling language, a high-level class of Petri nets, Java programming language as the annotation language, and free tool support. The model can be used to perform software-level simulations and can also be interconnected to existing physical devices using Internet of things technologies, enabling interactions between Cyber–Physical Systems (CPSs). It thus allows for the control of the shop floor and the reuse of the current machine park to make its adoption more sustainable. The model was used to generate several simulation results, which are presented and analyzed, thus demonstrating the model’s usefulness.