Background: Conflicting interests, power imbalance and relationships characterized by distrust are just a few of the many challenges community–academic research partnerships face. In addition, the time it takes to build relationships is often overlooked, which further complicates matters and can leave well-intentioned individuals re-creating oppressive conditions through inauthentic partnerships. This paper presents a novel approach of using meeting minutes to explore partnership dynamics. The Community Assessment of Freeway Exposure and Health (CAFEH) partnership is used as an illustrative case study to identify how community academic partnerships overcome the challenges associated with community-based participatory research (CBPR). CAFEH is a study of ultrafine particle exposure (UFP) near highways in the Boston, MA area. Methods: Qualitative analysis was applied to meeting minutes and process evaluation reports from the first three years of the CAFEH study (n = 73 files). In addition, a group meeting was held with project partners in order to contextualize the findings from the document analysis. Results: The three most commonly referenced challenges included language barriers, the overall project structure and budgetary constraints. Meanwhile, a heavy emphasis on process and an approach steeped in participatory democracy facilitated CAFEH’s ability to overcome these challenges, as well as sustain and augment strong partnership ties. Conclusions: This experience suggests that leadership that incorporates an organizing approach and a transformational style facilitates CBPR processes and helps teams surmount challenges.