The analysis of Regional Innovation Systems (RIS) in Latin America has grown from both academic and policy perspectives. However, the dominant structural approach on RIS has limited the scope of analysis, overlooking the functional dynamics that take place in such systems. This paper addresses the question of how to conceive the governance of RIS from a functional perspective, by conducting a case study on the emerging Risaralda RIS (Colombia), which stands out for its innovative performance while still displaying important systemic failures. We specifically inquire into the strengths, weaknesses, integration dynamics and functions of this RIS. Results show a system with institutional and governance failures, which is host to a disperse network of stakeholders and innovation processes that include prioritized and enabling functions. We discuss these results and propose a governance framework that was collectively outlined with the participation of stakeholders in the RIS of Risaralda.