Both cocoa and coffee are important cash crops that are usually interplanted under shade trees in agroforestry practices. Competition between roots of cash crops and neighboring trees remains a major knowledge gap. Ideal agroforestry shade trees would develop their root systems below the cocoa and coffee root zones, minimizing plant competition for nutrient uptake in the soil layers. Assessment of root development in soil remains highly challenging. Destructive excavation provides root biomass and root morphology data. However, it is not possible to identify the species of fine roots that are present in different soil zones in a mixed-species plantation. We selected two adjacent cocoa and coffee plantations where Canarium indicum was used as a shade tree. We used DNA meta-barcoding to determine the presence and abundance of fine roots of each species in the soil profile to a depth of 80 cm. Cocoa and coffee had higher fine-root abundance at 0-30 cm depth, whereas canarium had higher fine-root abundance at 30-80 cm depth. Our study indicated that canarium could be a suitable shade tree for cocoa and coffee. DNA metabarcoding allowed us to develop a deeper understanding of root development through the tropical soil profile and can be used to manage agroforestry systems.