Nowadays, manufacturing processes have become highly complex. Besides, more and more, governmental institutions require companies to implement systems to trace a product’s life (especially for foods, clinical materials or similar items). In this paper, we propose a new framework, based on cyber-physical systems, for developing traceability systems in small manufacturing companies (which because of their size cannot implement other commercial products). We propose a general theoretical framework, study the requirements of these companies in relation to traceability systems, propose a reference architecture based on both previous elements and build the first minimum functional prototype, to compare our solution to a traditional tag-based traceability system. Results show that our system reduces the number of inefficiencies and reaction time.