Considering the increasing interest in the incorporation of natural antioxidants in enriched foods, this work aimed to establish a food-grade and suitable procedure for the recovery of polyphenols from cocoa beans avoiding the degreasing process. The results showed that ultrasound for 30 min with particle sample size < 0.18 mm changed the microstructure of the cell, thus increasing the diffusion pathway of polyphenols and avoiding the degreasing process. The effect of temperature, pH, and concentration of ethanol and solute on the extraction of polyphenols was evaluated. Through a 24 full factorial design, a maximum recovery of 122.34 ± 2.35 mg GAE/g, 88.87 ± 0.78 mg ECE/g, and 62.57 ± 3.37 mg ECE/g cocoa beans, for total concentration of polyphenols (TP), flavonoids (TF), and flavan-3-ols (TF3), respectively, was obtained. Based on mathematical models, the kinetics of the solid–liquid extraction process indicates a maximum equilibrium time of 45 min. Analysis by HPLC-DAD-ESI-MS/MS showed that our process allowed a high amount of methylxanthines (10.43 mg/g), catechins (7.92 mg/g), and procyanidins (34.0 mg/g) with a degree of polymerization >7, as well as high antioxidant activity determined by Oxygen Radical Absorbance Capacity (1149.85 ± 25.10 µMTrolox eq/g) and radical scavenging activity (DPPH•, 120.60 ± 0.50 µM Trolox eq/g). Overall, the recovery method made possible increases of 59.7% and 12.8% in cocoa polyphenols content and extraction yield, respectively. This study showed an effective, suitable and cost-effective process for the extraction of bioactive compounds from cocoa beans without degreasing.