The increasing global competition within today's manufacturing industries is confronting organizations with interdisciplinary challenges that require intellectual expertise and innovative technological solutions in various knowledge areas. Research organizations and manufacturing companies can improve their overall performance by bundling expertise in collaborative innovation networks. For this purpose a systematic Benchmarking approach has been developed by Fraunhofer IPK to match the competencies and capacities within a pool of organizations in order to facilitate a sustainable cooperation in terms of resources, customers and R&D topics. Furthermore, a KPI-based identification of best performing network-partners allows an initiation of Best-Practice transfers to gain sustainable competitive advantages for the whole network. Based on a methodological approach, the identification of collaboration potentials and Best-Practices is supported by software tools that visualize the results in an understandable and applicable way.