South–North research collaborations are now commonly used in the field of climate and development to advance knowledge, inform decision-making and strengthen capacity in the global South. Southern leadership within these collaborations is widely seen as instrumental to their lasting impact. This study examines how Southern leadership and capacity were promoted in the Future Climate for Africa (FCFA) programme, a five-year initiative that sought to enhance resilience to climate change in Africa. Drawing on interview and survey data from programme participants, document analysis and experiential insights from the author team, we examine how Southern leadership was pursued within the programme, and the barriers that constrained action at a range of scales. Most climate and development initiatives, like FCFA, sit at the intersection of multiple social, political and research systems. To disrupt the structures that sustain the power of Northern institutions and obstruct change, funders must go beyond programme-level interventions such as funding and distribution of roles, and consider deeper leverage points of change. We propose how shifts in mindsets and metrics in relation to Southern leadership and capacity can contribute to this change.