Psychologists engaged in public health research and intervention will become more involved in multiple intervention programming approaches. Managing innovation and complexity is a challenge when the team members come from different disciplines, organizational cultures and research perspectives. This report captures some of those challenges with a participatory, capacity-building, community-based intervention over research stages. We detail successful and less successful attempts to manage the challenges within changing public health contexts and end with concrete suggestions for teams with mixed intervention and research goals. Insights from this project should inform similar programmes with multi-level, participatory, community-based approaches.