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Community-based participatory research (CBPR) is a growing practice by which academics and community partners conduct collaborative health-based research. While CBPR fosters productive partnerships, there is increasing research on interpersonal group dynamics and the ways that intersecting factors, such as gender and ethnicity, affect the social interactions within CBPR. This paper explores the tensions inherent in large interdisciplinary community-based participatory research partnerships, through the examination of a long-standing community–academic partnership focused on advancing public health. Nine qualitative interviews were conducted between November 2019 and January 2020 with steering committee members from a long-standing collaborative partnership that conducts research to inform public health action. While the collaborative process was generally positive, we also uncovered less pleasant aspects of CBPR projects that are infrequently discussed in the literature, such as role confusion and power dynamics. Leadership style was seen as the driving force shaping how other team concerns were perceived. Not having structures in place to facilitate relationship development, or clear documentation of procedures, rules and norms, led to team complications. Team members suggested that a renewed focus on organisational structure would contribute to role clarity and organisation. The results highlight the complexity of working on interdisciplinary mixed community–academic teams, specifically the ways in which interdisciplinary, collaborative research can be a complicated, meandering process, often without clear-cut answers to sometimes simple questions.