A vibrant ecosystem of innovation hinges on undergraduate science programs that inclusively deepen conceptual understanding, develop scientific competencies, and spark wonder and appreciation for science. To create this ecosystem, we need to influence multiple components of the system, including faculty as well as culture (i.e., rules, goals, and beliefs giving rise to them). Here we describe and evaluate a multi-institution community of practice focused on transforming undergraduate biology programs' organizational practices, behaviors, and beliefs, as well as instilling a sense of agency in community participants. The approach drew on three change theories: Community of Practice, Participatory Organizational Change, and Organizational Justice. Via mixed methods, we found that participation in the community catalyzed the flow of tangible capital (knowledge resources), grew social capital (relationships and identity), and developed human capital (creative problem-solving and facilitative leadership skills; sense of agency). In participants' home departments, application of knowledge capital was associated with increased implementation of the principles of the Vision and Change report. Departmental change was enhanced when coupled with use of capitals developed through a community of practice centered on creative problem-solving, facilitative leadership, conflict resolution, and organizational justice.