The health benefits of cocoa depend on the flavan 3-ols, procyanidins, and methylxanthines, which decrease from the early stages of cocoa bean processing. The objective of this research was to obtain a cocoa extract high in these compounds with (-)-epicatechin as the primary reference. An evaluation of two pretreatments of cocoa beans with a control after harvesting was made: A (untreated/control), B (Frozen), and C (Polyphenol oxidase inhibition), all followed by dehydration at 45 °C until obtaining a cocoa powder. In terms of (-)-epicatechin content, the best pretreatment was put on to a hydroalcoholic extraction. Flavan 3-ols, procyanidins, methylxanthines, and total polyphenols content (TPC), were quantified in the cocoa powders and the hydroalcoholic extract. The results showed that the control (A), significantly conserves the (-)-epicatechin (24.964 ± 0.400 mg/ g) ca. 7 times more than conventionally sun-dried and fermented beans (3.742 ± 1.977 mg/g) ca. The hydroalcoholic extraction increased the (-)-epicatechin ca. 3 times more based on pretreatment A (84.738 mg/g).