Drawing on the triple helix framework and organizational institutionalism, this article applies a qualitative research approach to analyze structures, institutional logics, power relations that shape inter-organizational relations and the structuration of a knowledge production system in an emerging economy. Findings highlight the emergence of a fifth-helices knowledge production system includes the state, science and education, industry, international actors, and society. The system comprises two major segments, one associated with the traditional command economy and characterized by institutional control that reproduces an ill-adopted and less transparent system based on systemic power. At the border of this system, a marketand quality-oriented segment emerges through marked-oriented evolution and collaborative co-evolution processes driven by institutional agency. The system-level dynamics are characterized by political ambidexterity that enables the state to maintain control by privileging traditional science and education constituencies, and at the same time support the transition of the knowledge production system towards international methodology and quality standards through relational mechanisms such as cooperation, harmonization, and partnership. Our research shows that the proposed framework offers a valuable basis for deriving realistic policy and program recommendations to guide national and international actors in designing interventions and collaboration within knowledge production systems in developing countries.