Citrus are important fruit crops of high economic and ecological importance in southern Cameroon. Smallholders usually plant citrus in complex cocoa-based agroforests (CBAS). Health and productivity of citrus are generally jeopardized by a wide range of pests and diseases for which environmental conditions can be critical drivers. An assessment of the effects of two structural characteristics of CBAS on citrus tree decline (CTD) intensity and six pests and diseases that induce it was conducted in 26 farms. The study was carried out in four citrus-growing basins in the Centre Region of Cameroon between June and September 2016. Observations were made by visual recognition of CTD, as well as disease symptoms and pest damage. Their intensity or abundance was assessed using a scale ranging from 1 to 4. Depending on the situation of citrus trees in the CBAS and with regard to the upper strata, three shade level (dense, moderate and no shade), and three spatial structural patterns (aggregate, random and regular) were defined. Results showed that, CTD intensity under dense shade conditions was significantly low (P < 0.001), as compared to those in moderate and no shade conditions. Plots with aggregated or random spatial structure of citrus trees showed significantly higher CTD intensities (P < 0.001) compared to those with a regular spatial structure of citrus trees. The involvement of CBAS structural characteristics in CTD regulation has been demonstrated and could contribute to the development of an integrated management tool for citrus pests and diseases in an associated crop context.