Up to the present time, the control software design of production systems has been developed to produce a certain number of goods, in a centralised manner and through a case-by-case, timely and costly process. Therefore, the current control design approaches hinder factories in their pursuit to acquire the essential capabilities needed in order to survive in this customer-driven and highly competitive market. Some of these vital production competencies include mass customisation, fault tolerance reconfigurability, handling complexity, scalability and agility. The intention of this research is to propose a uniform architecture for control software design of collaborative manufacturing systems. It introduces software components named as modular, intelligent, and real-time agents (MIRAs) that represent both intelligent products as clients (C-MIRA) and machines or robots as operators (O-MIRAs) in a production system. C-MIRAs are in constant interaction with customers and operators through human machine interfaces, and are responsible for transforming products from concepts up to full realisation of them with the least possible human intervention. This architecture is built upon the IEC 61499 standard which is recognised for facilitating the distributed control design of automation systems; however, it also takes into account the intelligent product concept and envisages the machines’ control to be composed of a set of modular software components with standardised interfaces. This approach makes the software components intuitive and easy to install, to create the desired behaviour for collaborative manufacturing systems and ultimately paves the way towards mass customisation. A simplified food production case study, whose control is synthesised using the proposed approach, is chosen as an illustrative example for the proposed methodology.