It is understood that through biodiversity, several ecosystem services are provided and maintained, and in turn, these services provide sustainability and resilience to the ecosystem, as well as additional benefits to humanity. My thesis focuses on the Pest and Disease (P&D) regulating service. This service helps to regulate the appearance, incidence, and severity of P&D in plants within the system. The pathways and mechanisms involved in the provision of this service are still not well described; therefore, we hope to answer the following question: Does biodiversity impact the P&D regulating services in agroforestry systems? To answer this question, we propose the use of an integrated indicator to assess the P&D regulating services introduced into cocoa agroforestry systems through the addition of biodiversity. Theoretically, it is possible to estimate the service by measuring the yield losses due to P&Ds, as it is a direct result of the interactions of the system. We also propose that because agroforestry systems may be spatially heterogeneous, by combining the indicator with spatial approaches, we will identify specific areas of interest within the agroforestry plots. By characterizing the biological compartments that compose these areas, we will better understand the mechanisms and pathways that are involved and influence the P&D regulating service. We propose to answer our question within a cocoa agroforestry system framework in which the P&D complex is a major loss factor for production. The study site is located in the Alto Huayabamba Valley in the San Martin Region in the Peruvian Amazonia, where the cocoa varieties and organic management strategies are largely the same and allow unbiased testing of our methodology.