A widely held assumption is that intensifying agroforestry will lead to sustainable increases in production, societal resilience and food security, urgently needed in the current context of changes in markets, climate and demography. Current thinking assumes that to achieve sustainable innovation a participatory approach with public, civil and private stakeholders is necessary, combined with a systemic, trans-disciplinary approach, rather than a technical approach. This study presents a case of applying the Theory of Change (ToC) concept to test this assumption. The ToC was designed to articulate the process of scaling of action-research findings, and to adapt the research to the context of complex agroforestry systems at plot, household, farm, village and landscape levels. This allowed to develop an intervention logic that unpacks what sustainability means for farmers and other local stakeholders in four West African agroforestry systems. The conceptual approach created an awareness of potential impacts of scaling initiatives based on a ToC with pathways to impact combined with monitoring the effects of the research & development project on a variety of ecological, agronomic and economic performance indicators. A number of constraints and paradoxes that are linked to current research and development short term funding are also discussed.