Cocoa and its derivatives are widely recognized for their health benefits due to the presence of bioactive compounds such as polyphenols and methylxanthines, which possess antioxidant and anti-inflammatory properties. However, the concentration of these compounds in cocoa beans is significantly influenced by the genotype and post-harvest processing conditions, such as fermentation and drying. This study investigated how the bioactive compounds of cocoa beans from 18 genotypes from Pará are influenced by genetic variations before and after fermentation and drying. The cocoa beans were fermented with starter cultures of Pichia kudriavzevii, Lactiplantibacillus plantarum, and Acetobacter pasteurianus for six days and then sun-dried to achieve <8% moisture content. The degree of fermentation was evaluated by a cut test and fermentation index. Extraction was performed sequentially using methanol and acetone as solvents, and the quantification of the methylxanthines, flavan-3-ols, procyanidins, flavonols, anthocyanins, and phenolic acid was carried out using ultra-high-performance liquid chromatography coupled with mass spectrometry (UHPLC-MS/MS). Theobromine was the predominant compound (mean of 22.89±4.08mg/g), with an average reduction of 20% after fermentation, while caffeine decreased by 25.16%. Among the flavan-3-ols, epicatechin had the highest concentration (mean of 16.52±4.57mg/g), reducing by 77.35%. Procyanidins, particularly procyanidin B2, showed an average reduction of 69.25%. Anthocyanins underwent rapid degradation, with losses up to 93%. Flavonols showed small variations, while protocatechuic acid increased in fermented and dried beans. The chemical differences between fermented and unfermented beans overshadow the differences among genotypes, but some of them stood out with high levels of bioactive compounds, such as CCN51, CAB270, CAB324, and MA11, suggesting great potential for the development of nutraceutical and functional products. These results highlight the importance of considering genotype and post-harvest processing conditions to optimize the bioactive compound content in cocoa beans, promoting health benefits and adding value to the functional food market.