Building evaluation capacity within an organization promotes its effectiveness and remarkable changes. The Puerto Rico Clinical and Translational Research Consortium (PRCTRC) is a research infrastructure among three major medical and health education institutions in Puerto Rico. Complex research programs, as PRCTRC, require mixed evaluation practices encouraging continuous quality processes, and providing opportunities for reflections, learning, and growth. This study will describe a conceptual framework to build evaluation capacity in a complex setting integrating a participatory evaluation approach, organizational learning practices, and continuous quality improvement processes. This framework has been exemplary to advance the development of high-level evaluation capacity, providing critical data about program performance, management competencies, organizational functionality, and impact. Diverse, useful and relevant experiences of evaluation practices will be discussed, focused on the capacity developed by each element of this framework. Furthermore, recommendations for specific steps and actions to create evaluation capacity in a complex research structure will be presented.