Community-academic partnership research is a fairly new genre of community-based participatory research. It has arisen in part, from recognition of the potential role of alliances in the development and translation of applied knowledge and the elimination of health disparities. This paper reports on the learning process of academic and community members who worked together in developing a logic model for a research program focusing on partnerships with vulnerable populations. The Partners in Community Health Research is a 6-year training program that seeks to combine research, training, and practice through the work of its "learning clusters". As these types of partnerships proliferate, the articulation and exploration of clear models will assist in their implementation. The authors, coming from both academia and community agencies, present a logic model meant to facilitate program management. Key considerations in the model's development are discussed in the context of an ongoing research partnership; namely, the complexity of the research partnership, power and accountability, alignment with health promotion policy, and the iterative nature of program design. Recommendations challenge academics, policy-makers, service providers, and community members to reflect on the elements needed to support and manage research partnerships and the tools necessary to ensure continued collaboration.