Cocoa bean is a resource with great level of bioactive components that have shown potential beneficial effects on health, in addition to being the main ingredient in the chocolate industry. This study evaluated the total antioxidant capacity (quencher-DPPH°), polyphenols, fatty acid profile, and chromatic parameters of Peruvian commercial cocoa beans. The different analytes were quantified using UV–Vis absorption spectroscopy, gas chromatography-flame ionization detection (GC/FID) and liquid chromatography coupled with diode array detector (HPLC-DAD). Results showed that the lightness (L*) and the hue angle (hab) were the greatest variation in both cocoa kernel and cocoa powder. The main fatty acids were oleic, stearic, and palmitic (respective averages of 34.48 ± 1.49, 31.81 ± 1.51 and 30.01 ± 0.89%). Theobromine (9.79–12.95 mg/g), catechin (3.90–18.22 mg/g) and epicatechin (6.15–13.09 mg/g) represented the major bioactives. Also, hybrid cultivars (Hy1, Hy2, Hy3, Hy4, Hy5, and Hy6) provided the highest content in polyphenols, flavonoids, and flavanols, also resulting in the highest total antioxidant capacity.