Agroforestry is a sustainable land-use strategy that requires better integration of diverse knowledge systems. This paper examines how formal knowledge systems for cacao agroforestry systems in Colombia are structured, and how farmers understand and manage these systems. We interviewed 42 actors involved in knowledge production and dissemination and worked with 18 farmers to create mental maps of their management practices. Our findings show that formal knowledge systems remain predominantly top-down and scientific-based, despite increasing recognition of local knowledge. Farmers' mental models reflect this, showing reliance on external advice and simplified cause-and-effect thinking. When theoretically pooling farmers' perspectives, we observe a more comprehensive understanding of agroforestry, suggesting that social learning can strengthen their independence and adaptive capacity. Moreover, farm management is shaped by context-dependent variables such as climate seasonality and market access, thus highlighting the importance of integrating farmers' experiential knowledge into agroforestry design and dissemination for more sustainable, context-sensitive decision-making.