Cocoa beans of the CCN-51 clone harvested in the Tumaco region (Nariño, Colombia) were fermented following four different treatments: (1) spontaneously (at room temperature for 120 h) in traditional conditions (Control); (2) traditional processing with a pre-drying (sun-dried for 24 h) treatment (PD); (3) with fermentation (for 120 h) after inoculation of a yeast starter culture (YS); and (4) including both treatments, pre-drying and yeast inoculation (PD+YS). Chemical composition, fatty acids, total polyphenol, methylxanthines (theobromine and caffeine) and lactic acid content of cocoa beans were determined. Chemical and fatty acid composition and theobromine content were not affected by the different fermentation treatment applied. When analysing total polyphenol content, YS and PD+YS treatments significantly increased the content of these compounds at the end of the fermentation process, while PD treatment decreased the caffeine content of cocoa beans. Finally, lactic acid content decreased as a consequence of both inoculation of yeast starter and mainly the pre-drying treatment. In conclusion, solar pre-drying in the open air and the inoculation of a yeast starter treatments could improve the final quality of coca beans.