Tropical agroforestry systems are recognized as an attractive way to reconcile productivity and ecosystem services without compromising the agrosystem. However, to optimize ecosystem services, the structure of existing agroecosystems must be improved to enhance interactions within them. In this study, we evaluated the combined effect of shade rate and spatial structure of citrus trees in cocoa-based agro-forestry systems (CBAS) on Phytophthora foot rot disease (PFRD). A set of 33 CBAS of 2500 m2 was established in five citrus production basins in the humid forest zones of Cameroon. The citrus spatial structure was analyzed by the Ripley method. Field data, including the specific composition of the experimental plots, the tree’s geographical position, as well as their structural characteristics, were used to reconstruct CBAS in 3D. Subsequently, citrus trees were divided into 9 treatments based on the amount of shade they received (dense shade, light shade, or no shade) and their spatial structure (regular, aggregated, or random) in the CBAS. PFRD intensity was calculated by measuring the extent of the PFRD lesion relative to the circumference of the citrus crown. Citrus trees with a regular spatial structure, and located under dense or light shade showed low PFRD intensity. Citrus trees with an aggregated spatial structure, regardless of their shade situation, as well as those with a random spatial structure and no shade, showed high PFRD intensity compared to all other treatments. These results show that appropriate management of shade rate and spatial structure in CBAS can significantly contribute to the control of PFRD and thus promote citrus production in complex agroforests. For the first time, it is demonstrated that optimizing the combined effect of shade rate and spatial structure of associated trees would allow the design of optimal models of resilient agroforestry systems, capable of self-regulating pests and reducing chemical pesticide use.