In this work, we explore the dynamics of microfoundations dimensions (individuals, processes and structures) of research organizations (ROs) in order to diagnose the challenges faced by researcher management in Brazilian ROs and improve cooperative actions. To this end, analytical variables were defined from the theoretical fields of management (people and microfoundations) and research-industry cooperation, and applied in three exploratory-descriptive case studies. The results show that the effectiveness of research-industry cooperation depends on paradigm shift and long-term actions, such as the implementation of a collaborative organizational culture and the prioritization of innovative governance. Furthermore, the development of these capacities is hampered by the low maturity of career development processes, structural and financial-budgetary constraints. This research contributes to theoretical development, establishing constructs from the ROs specificities and proposing initial relationships among the analytical variables structured. For practice, we highlight the organizational diagnosis and actions for a better cooperative performance of ROs.