Main researches and developments in IMS, MAS (Multi-Agent System) and HMS (Holonic Manufacturing System) for manufacturing plant control and management as well as manufacturing enterprise networking are based on ICTs (Information & Communication Technologies) based approaches. Beyond these technology-driven approaches, the field of ‘Intelligence in Manufacturing' requires sound scientific foundations in order to meet systematisation in modelling as originally addressed by (Yoshikawa, 1995). In this way, this paper deals with principles and elements of the Category Theory as a coherent mathematical framework in order to move to more prescriptive and ‘bottom-up' modelling approaches able to better understand and model the dynamical emergent properties of new agile manufacturing systems.