The health and productivity of citrus are generally jeopardized by a host of diseases, for which the environmental conditions of the cropping system are critical drivers. Several studies conducted on various diseases of perennial crops have shown the involvement of the structural futures of the cocoa-based agroforestry system (CBAFS) in the spread of pathogens and the epidemics development. This chapter highlights the effect of the CBAFS’s structural characteristics on the intensity of three citrus diseases in the humid forest zones of Cameroon. The involvement of CBAFS structural characteristics in diseases regulation is demonstrated. In particular, the spatial structure of citrus in agroforests shows an effect on the spread of diseases. Moreover, distribution of citrus in the CBAFS, with minimum spacing of 12 m between citrus trees, limits the damage caused by Pseudocercospora leaf and fruit spot disease (PLFSD) and citrus diseases caused by Phytophthora (CDP). Dense shading helps to minimize the intensity of diseases such as CDP and PLFSD and Citrus scab disease. This work may make it possible to contribute to the development of an integrated management tool for citrus diseases in an associated crop context.