The involvement of spatial structure in pathogen regulation in complex and biodiverse agroforests has been demonstrated in several studies. It is thus recognized that the aggregated spatial structure of host populations leads to the rapid dispersion of pathogens. To lead farmers to adopt regular spatial structures that are less conducive to pathogen dispersal, an upstream understanding of the reasons for adopting existing spatial structures is crucial. To this end, semi-structured surveys were conducted among farmers in four citrus production basins in the humid forest zones of Cameroon. The farmer's profile was drawn up and cocoa-based agroforestry systems (CBAS) management strategies in relation to the spatial structure were examined. Subsequently, CBAS were mapped and the effective citrus spatial structure within them was analyzed using the Ripley method. The involvement of endogenous and exogenous factors determining citrus spatial structure was highlighted. It was found that citrus spatial structures reported by farmers and checks on the CBAS showed inconsistencies. Somehow beyond the farmers' control, endogenous factors such as the number of individuals and species diversity of the plant stand, are the ones that determine citrus spatial structures in the CBAS. It, therefore, appears that citrus spatial structures in the CBAS are more related to the structural characteristics of the systems than to the farmer's deliberate action. Appropriate spatial structures can be adopted, provided that farmers are well-informed and trained in modern agroforestry techniques.