This paper describes and discusses the essential pedagogical elements of the Partnering in Community Health Research (PCHR) program, which was designed to address the training needs of researchers who participate in collaborative, interdisciplinary health research. These elements were intended to foster specific skills that helped learners develop research partnerships featuring knowledge, capabilities, values and attitudes needed for successful research projects. By establishing research teams called “clusters”, PCHR provided research training and experience for graduate students and post-doctoral fellows, as well as for community health workers and professionals. Pedagogical elements relied on active learning approaches such as inquiry-based and experience-based learning. Links between these elements and learning approaches are explained. Through their work in cluster-based applied research projects, the development of learning plans, and cross-cluster learning events, trainees acquired collaborative research competencies that were valuable, relevant and theoretically informed.