Pathogen dynamics in agroforestry systems result from several mechanisms and interactions whose independent effects are difficult to delineate. In recent decades, it has been shown that shade, as a structural feature in agroforestry systems, influences the spread of pathogens through its physical and biological effects. In Cameroon, citrus trees are mainly grown in cocoa-based agroforestry systems (CBAS), and are threatened by a variety of pathogens. This study examines how shading modifies the microclimate in the local environment of citrus trees in CBAS, and the resulting effect on citrus foot rot disease (PFRD). The study was conducted in the Cameroon agroecological zone with bimodal rainfall, where a network of 20 CBAS plots was established. Primary cartographic and structural data were used to perform static simulations with cumulative shadow overlay in ShadeMotion software. A soil sensor was used to quantify the microclimate by measuring air temperature and relative humidity above and in the soil, as well as soil pH. Relationships between shade rate, microclimatic variables, and PFRD intensity were investigated. Results showed that the effect of temperature on PFRD was independent of shade rate. A dependency relationship between relative humidity above and in the soil and PFRD according to shade rate was found. Indeed, a positive correlation of PFRD with relative humidity was observed for citrus trees located in full sunlight, while a negative correlation was observed for citrus trees located under dense and light shade. Optimization of structural characteristics of CBAS would allow ecological management of PFRD and reduction in the use of chemical pesticides.