Cacao pest and diseases (P&Ds) infect and affect their hosts in specific ways, which adds complexity to study their global impact on production. Commonly, incidence is used as an indicator to evaluate P&Ds, however, it does not provide any information on yield loss, whether we look at it as a loss in quantity or quality. Therefore, from an agronomic point of view, incidence is not enough to evaluate the impact and the damage of P&Ds over production. By focusing on three specific P&Ds (Black Pod disease, Frosty Pod Rot and the "Mazorquero", local name for the American Cocoa Pod Borer) within the P&D complex that affect the cocoa pod in the Peruvian Amazonia, this research aims to produce a simple and replicable model that will allow to estimate more accurately the P&Ds incidence related yield loss and help us simulate different scenarios to calculate crop loss under different market situations. To evaluate the amount of damage caused by these P&Ds, 30 pods were opened per monitored P&Ds (each set infected with either one or a combination of the P&Ds outlined above), totalling 120 pods for the four evaluated P&Ds combinations on the CCN-51 cacao variety. Then the seeds were counted and classified in Healthy (unaffected), Affected (affected by disease but still usable) and Destroyed (unusable due to disease) to establish a Seed Damage Ratio (SDR) for each disease and disease combination. Furthermore, we elaborated a model that combines the SDRs and P&D's incidence per plot to have an estimation of the yield loss at plot scale. Our results show that the Black Pod and the Mazorquero, as well as their combination, tend to cause the least amount of damaged seeds, while the Frosty Pod Rot tends to cause the most damage. Black Pod and Mazorquero tend to have similar impact, showing mixed results between healthy and usable seeds, while their combination has a bigger impact with more usable than healthy seeds. By modifying the yield loss model for the plot, two simulations of different scenarios predicting the crop loss were elaborated. These showed that the P&D composition is highly relevant for crop loss estimation and the SDRs allow to take into consideration this composition for integrated P&D management. Keywords: Pest and Diseases; Incidence; Yield Loss; Seed Damage Ratio.