The intention of this research is to propose a uniform architecture for control software design of collaborative manufacturing systems. It introduces software components known as Modular, Intelligent, and Real-time Agents (MIRAs) that represent both products (C-MIRA) and mechatronic components (O-MIRAs) in a production system. C-MIRAs are in constant interaction with customers and operators through human machine interfaces (HMIs), and are responsible for transforming products from concepts up to full realization of them. It is demonstrated that desired services of a number of machines and mechatronic components can be dynamically allocated to a C-MIRA using a fully decentralized scheduling and operation control. This architecture also envisages the machines’ control to be composed of a set of modular software components, with standardized interfaces. This makes them intuitive and easy to install, to create the desired behavior for collaborative manufacturing systems. A simplified food production case study, whose control is synthesized using the proposed approach, is chosen as an illustrative example for the proposed methodology.