The role of agroforest systems in pathogen regulation through structural characteristics such as shade and tree diversity is recognized. However, few studies have examined the importance of these factors on the spread of diseases of associated fruit trees in agroforestry systems, especially cocoa-based agroforestry systems (CBAS). The aim of this study was to evaluate the effect of associated tree diversity and shade rate into CBAS on citrus Phytophthora foot rot disease (PFRD) intensity. The study was carried out in five citrus production basins of Cameroon, contrasted by ecology and rainfall regimes. A set of 33 CBAS plots was mapped and their species composition and vertical structure were determined. Field data were used to reconstruct CBAS in 3D with Shademotion 5.1.47 software. Using static simulations with shadow overlays, shade rate received by each citrus tree was calculated. Subsequently, citrus trees were grouped into three categories according to the shade rate they received: (i) full sun, with shade rate <30%; (ii) light shade with shade rate 30–70% and, (iii) dense shade, with shade rate >70%. PFRD intensity was determined by measuring the canker extent relatively to the citrus crown circumference. A significant difference in PFRD intensity was observed between the different shade rates. Citrus trees receiving no shade were significantly more attacked by PFRD than those receiving little shade or dense shade. The antagonistic effect of shade was demonstrated. At the expense of factors related to the specific composition of the CBAS, shade, temperature, relative humidity and rainfall were found to be the main factors explaining PFRD intensity in CBAS. This study shows that microclimatic alterations due to the biodiversity in tropical agroforestry systems contribute to sustainable pest management.