Scholars have enumerated unique challenges to collaborative interdisciplinary research, many of which evade prescriptive solutions. Some of these challenges can be understood as "essential tensions," necessary and persistent contradictory imperatives in the scientific process. Drawing from interviews with internationally renowned interdisciplinary environment-society research center leaders primarily located in United States academic institutions, we identified three hierarchical tensions in collaborative interdisciplinary research: (1) an epistemic tension between knowledge generation processes that blend multiple approaches into one unified intellectual perspective versus pluralistic processes that maintain multiple, discrete intellectual perspectives, (2) a structural tension between organizations that provide stability to persist and build unified knowledge, while maintaining the flexibility to experiment with novel organizational arrangements that foster innovation, and (3) "affective" tensions for individual researchers between the security of working within cohesive research communities versus attraction to the creative challenges in new intellectual communities. Our results indicate that these tensions are interdependent, similar to previous observations that disciplinary and interdisciplinary knowledge productions are linked. Rather than attempt to resolve tensions between dueling directives, leaders of interdisciplinary research centers can manage essential tensions with purpose through process-oriented and self-reflective management of the unique epistemic culture of the research centers they lead.