Most of SMEs are engaged in open innovation practices, but they do not benefit from open innovation or from patenting in the same way as larger firms do. At the same time SMEs, as territorialized suppliers, play a crucial role within evolving regional specialization. In this context the purpose of our study is to examine how low and medium technology supplier SMEs learn and organize themselves at a territorial level to address the challenge of IP protection in an open innovation paradigm. We used a qualitative method with a longitudinal multi-case study involving 27 companies with a historical lance to compare the territorial dynamics of knowledge protection within clustered supplier SMEs in two European regions. The results show they protect their knowledge by learning how to design, in a direct relationship with clients, customized complex technological products to develop a new organizational matrix of multidisciplinary knowledge that reveals itself difficult to imitate within the clusters. They also cope with other supplier firms across sectors even if they show societal path dependencies in the way to build cooperation. This dynamic has given birth to changing structural relationships among regionally clustered SMEs and between them and large firms.