Cocoa pods are harvested and split open to release the beans. The beans are embedded in a pulp. When the pods are broken the beans and pulp are sterile but they become contaminated with a variety of microorganisms from the pods, labourers hands, insects, vessels used for transport, etc.

The pulp surrounding the beans undergoes a fermentation process, which develops the colour and flavour of the beans. The initial anaerobic, low pH and high sugar conditions of the pulp favour yeast activity. Some research carried out revealed 24 strains of yeast on fermenting cocoa; another research by Rombouts identified 16 species. The fermentation process begins with yeasts converting sugars in the pulp to alcohol and carbon dioxide. Bacteria then start oxidising the alcohol into lactic acid and then, as conditions become more aerobic, acetic acid. This produces heat and raises the temperature in the first 24 hours. As the pulp breaks down and drains away bacteria continue to be active until fermentation is complete. The yeasts found during cocoa fermentation come from the surrounding environment, e.g., soil, trees etc. The species most frequently found at this stage are the Saccharomyces spp (in particular S. cerevisiae, Candida krusei, Kloeckera apiculata, Pichia fermentans, Hansenula anomola and Schizosaccharomyces pombe ). Research by Hansen and Welty shows that yeasts multiply very rapidly during fermentation and are able to survive drying and storage. One can find up to 107 yeast/gram in stored beans. After fermentation the cocoa beans are dried.

During the subsequent processing of the cocoa beans the beans are cleaned and can then undergo a form of thermal pre-treatment to separate the shell from the bean. One form of thermal pre-treatment uses infrared technology in which the beans undergo infrared radiation on a fluidised bed or vibrating conveyor. Water accumulates on the surface of the bean and bursts the shell. The high surface temperature induced by this process brings about a drop in the amount of microbiological contamination, especially yeast and other fungi. The beans are then separated from the shells and roasted. Following roasting the beans are turned into cocoa mass by grinding.

The quality of the cocoa mass is important due to the natural variability that exists in cocoa. Quality criteria for cocoa mass include figures for the number of yeasts found per gram - maximum 50 and for alkalised cocoa powder - a normal maximum of 50 with a limit of 100.