There has been substantial research on shade in cacao agroforestry systems, with most studies focusing on the impact of the shade cast by the associated shade trees on microclimate and yield. However, to our knowledge, no cacao agroforestry studies have explored how shade and its microclimate-modifying capacity influence the agrosystem's pest and disease regulating service. Utilizing thermal hygrometers and hemispherical photographs, we measured temperature and relative humidity during the dry and wet seasons as well as the shade of associated trees (associated shade), combining the latter with cacao self-shade (total shade). This approach enabled us to uncover how each shade type influences microclimate, yields, and pests and diseases beneath cacao trees. Additionally, we developed a novel method to estimate attainable yield, actual yield, and yield loss due to pests and diseases. Using yield loss as a proxy of the pest and disease regulating service and structural equation modeling, we built a model depicting the interaction network between shade types and their role in cacao pest and disease regulation. Our results showed that each shade type uniquely influenced cacao agroecosystem outcomes, with the associated shade negatively impacting attainable yield and total shade having a positive effect. Associated shade also mitigated the dry season microclimate and limited pest and disease occurrence. Notably, shade alone was not the sole pest and disease-related yield loss driver; it is part of a complex interaction network. These innovative shade measurement and yield loss estimation methods have enhanced enhance our understanding of pest and disease regulation. Conclusively, different management approaches for associated shade and total shade are crucial for optimizing yields and pest and disease regulation in cacao agroforestry systems.