Background: Community-Based Participatory Research (CBPR) is an approach in which researchers and community stakeholders form equitable partnerships to tackle issues related to community health improvement and knowledge production. Our 2012 realist review of CBPR outcomes reported long-term effects that were touched upon but not fully explained in the retained literature. To further explore such effects, interviews were conducted with academic and community partners of partnerships retained in the review. Realist methodology was used to increase the understanding of what supports partnership synergy in successful long-term CBPR partnerships, and to further document how equitable partnerships can result in numerous benefits including the sustainability of relationships, research and solutions. Methods: Building on our previous realist review of CBPR, we contacted the authors of longitudinal studies of academic-community partnerships retained in the review. Twenty-four participants (community members and researchers) from 11 partnerships were interviewed. Realist logic of analysis was used, involving middle-range theory, context-mechanism-outcome configuration (CMOcs) and the concept of the 'ripple effect'. Results: The analysis supports the central importance of developing and strengthening partnership synergy through trust. The ripple effect concept in conjunction with CMOcs showed that a sense of trust amongst CBPR members was a prominent mechanism leading to partnership sustainability. This in turn resulted in population-level outcomes including: (a) sustaining collaborative efforts toward health improvement; (b) generating spin-off projects; and (c) achieving systemic transformations. Conclusion: These results add to other studies on improving the science of CBPR in partnerships with a high level of power-sharing and co-governance. Our results suggest sustaining CBPR and achieving unanticipated benefits likely depend on trust-related mechanisms and a continuing commitment to power-sharing. These findings have implications for building successful CBPR partnerships to address challenging public health problems and the complex assessment of outcomes.