Polyphenol Extracts (PE) hold antioxidant properties, which might be related to positive effects on human health. It has been stated that PE, obtained from cocoa beans, contain fractions of flavan-3-ols with different degrees of polymerization (DP). However, it is unknown which of the fractions or their mixture drives the best antioxidant activity. This paper reports the study conducted to elucidate the role of each fraction (with different DP) on Antioxidant Capacity (AC). First, the process of extraction and separation of polyphenols’ fractions in cocoa beans was executed; afterward, AC was determined for each fraction individually and their combinations (monomers, dimers and oligomers). Solid-liquid extraction was made by using a 50% (v/v) ethanol solution and a mass:solvent ratio of 1:120 in an ultrasound bath. PE were separated into monomers, dimers, and oligomers by HPLC using a semipreparative column. The results obtained show that PE contain 95.35, 7.45, and 21.75 mg EE (epicatechin equivalents) / g ds of monomers, dimers, and oligomers, respectively. Finally, the AC of each fraction was evaluated using a complete cubic model mix design. According to the results, the best AC was obtained for dimers. However, when monomers, dimers and oligomers were mixed, an antagonistic effect on AC was observed.