Fermentation can be carried out in a variety of ways, but all methods depend on removing the beans from the pods and piling them together or in a box to allow micro-organisms to develop and initiate the fermentation of the pulp surrounding the beans. The piles are covered by banana leaves.

The fermentation process begins with the growth of micro-organisms. In particular, yeasts grow on the pulp surrounding the beans. Insects, such as the Drosophila melanogaster or vinegar-fly, are probably responsible for the transfer of micro-organisms to the heaps of beans. The yeasts convert the sugars in the pulp surrounding the beans to ethanol. Bacteria then start to oxidise the ethanol to acetic acid and then to carbon dioxide and water, producing more heat and raising the temperature. The pulp starts to break down and drain away during the second day. In anaerobic conditions, the alcohol converts to lactic acid but, as the acetic acid more actively oxidises the alcohol to acetic acid, conditions become more aerobic and halt the activity of lactic acid. The temperature is raised to 40ºC – 45ºC during the first 48 hours of fermentation. In the remaining days, bacterial activity continues under increasing aeration conditions, as the pulp drains away and the temperature is maintained. The process of turning or mixing the beans increases aeration and consequently bacterial activity. The acetic acid and high temperatures kill the cocoa bean by the second day. The death of the bean causes cell walls to break down and previously segregated substances to mix. This allows complex chemical changes to take place in the bean such as enzyme activity, oxidation and the breakdown of proteins into amino acids. These chemical reactions cause the chocolate flavour and colour to develop. The length of fermentation varies depending on the bean type, Forastero beans require about 5 days and Criollo beans 2-3 days.