Fermented and dried cocoa beans are the primary raw material for chocolate production. However, cocoa tree diseases (witches broom and black pod) and damages (mechanical or insect-induced) that lead to fruit rot can impact the quality of cocoa beans and their final products. This study aimed to understand the influence of damage caused by diseased (DF) or rotten (RF) fruit compared to healthy fruit (HF) on the protein, sugar, and lipid content of fermented and dried cocoa beans. Protein content (Lucas, Sotelo, 1980) and sugar composition, including sucrose, glucose and fructose, were analyzed by chromatography (AOAC, 2016). The lipid content was assessed by the Ankom method (AOCS, 2017). The lipid content varied significantly, with the RF sample showing the highest content (52.47±0.48%). The sugar profile, however, revealed notable differences, indicating significant metabolic changes in damaged and rotten beans. Sucrose content was higher in RF (1.10±0.05%) and DF (1.13±0.05%), possibly due to the inhibition of sucrose metabolism in diseased beans. The RF sample presented a higher concentration of glucose (0.36±0.01%) compared to HF and DF. Meanwhile, fructose levels were higher in HF samples (1.73±0.08%) compared to DF (0.60±0.05%) and RF (1.53±0.05%), suggesting the damage can cause alterations, whether by hydrolysis or other mechanisms. The protein content did not vary significantly among samples, with HF showing 15.35%, RF 15.17%, and DF 16.29%, suggesting that seed health status has a limited impact on the total protein content. This study reveals that the health status of cocoa beans significantly influences macronutrient composition, particularly in terms of sugar and lipid content. The lipid content was highest in rotten beans, and glucose and sucrose were more abundant in diseased and rotten beans than in healthy beans.