Biological collective systems have been an important source of inspiration for the design of production systems, due to their intrinsic characteristics. In this sense, several high level engineering design principles have been distilled and proposed on a wide number of reference system architectures for production systems. However, the application of bio-inspired concepts is often lost due to design and implementation choices or are simply used as heuristic approaches that solve specific hard optimization problems. This paper proposes a bio-inspired reference architecture for production systems, focused on highly dynamic environments, denominated BIO-inspired Self-Organising Architecture for Manufacturing (BIOSOARM). BIOSOARM aims to strictly adhere to bio-inspired principles. For this purpose, both shopfloor components and product parts are individualized and extended into the virtual environment as fully decoupled autonomous entities, where they interact and cooperate towards the emergence of a self-organising behaviour that leads to the emergence of the necessary production flows. BIOSOARM therefore introduces a fundamentally novel approach to production that decouples the system’s operation from eventual changes, uncertainty or even critical failures, while simultaneously ensures the performance levels and simplifies the deployment and reconfiguration procedures. BIOSOARM was tested into both flow-line and “job shop”-like scenarios to prove its applicability, robustness and performance, both under normal and highly dynamic conditions.