This article describes a mixed methods study of community-based participatory research (CBPR) partnership practices and the links between these practices and changes in health status and disparities outcomes. Directed by a CBPR conceptual model and grounded in indigenous-transformative theory, our nation-wide, cross-site study showcases the value of a mixed methods approach for better understanding the complexity of CBPR partnerships across diverse community and research contexts. The article then provides examples of how an iterative, integrated approach to our mixed methods analysis yielded enriched understandings of two key constructs of the model: trust and governance. Implications and lessons learned while using mixed methods to study CBPR are provided.