Abstract Access to heterogeneous knowledge resources is suggested in the literature as an important explanation of firm innovation and performance. The exchange of knowledge, however, can be a complex managerial challenge, especially between different epistemic communities. Our research focuses on the concept of epistemic communities to illuminate the complexity of tensions that arise in heterogeneous knowledge exchange in alliances, thus filling a gap in the literature. Using the Straussian grounded theory case study approach, our research investigates the emergence of horizontal, vertical, and inter-organizational epistemic tensions and explores management controls as instruments to guide the knowledge exchange in intermediary-driven research and development alliances. We find that the source of multiple epistemic tensions is rooted in the natural social behaviors of epistemic community members and further shows how these behaviors influence the effective use of inter-organizational management controls in facilitating heterogeneous knowledge exchange.