Delivering quality healthcare relies on well-functioning research and innovation processes in biomedicine. New treatments, diagnostic methods and prevention protocols have expanded the capacity of health systems to meet urgent and chronic health needs. However, medical innovation does not flow automatically from basic and clinical research to medical practitioners and patients. Indeed, policy initiatives aimed to foster collaborative research networks in biomedicine, which bring together multiple stakeholders, have permeated the policy agendas of public funding agencies worldwide. Despite these policy efforts, there is little systematic analysis of how research and collaborations processes work in practice. Accordingly, the aim of this study is to develop an integrated multi-criteria analysis and qualitative approach to assess the extent to which different types of research collaboration activities contribute to medical innovation. This paper presents a methodological approach that allows to measure the impact of collaboration activities on healthcare performance in the context of a biomedical research networks in rare diseases. The results demonstrate how the stakeholder management carried by a research group leads to the achievement of outputs prioritized by the research group.