Cocoa bean quality depends mainly on genetic material, edaphoclimatic factors and post-harvest processes such as fermentation. The impact of the fermentation process on the chemical and func-tional composition of different cocoa clones grown in southern Colombia was analyzed. A facto-rial design with repeated measures over time was used to analyze the effect of clone and fermen-tation time on chemical characteristics (bromatology, phenolic compounds and antioxidant ac-tivity). The bromatological characteristics showed significant differences between clones and fermentation time. Clones EET-8 and CCN-51 showed higher contents of acidity (0.51%), fat (63.61%), protein (12.85%) and carbohydrates (1.63 mg g-1). Moisture, acidity and sucrose in-creased their values between day 4 and day 6 of fermentation (P<0.05). Phenolic compounds and antioxidant activity had significant differences between clones, where clones CCN-51 and ICS-95 had high contents of phenols (64.56 mg g-1), flavonoids (3.30 mg g-1) and DPPH reducing capacity (325.55 µmol g-1). In this sense, we consider the FSV-41 clone as the major grain quality index based on the results of chemical composition at bromatological level, antioxidant activity and phenolic compounds.