The science of cacao fermentation 1: what happens during cacao fermentation?

Prior to being dried, cacao seeds (or “cocoa beans”) are fermented … or, more accurately, the fruity white pulp which envelops the beans is fermented.

Cacao fermentation doesn’t technically ferment the beans – it actually ferments the fruity white pulp which encases the beans.

The fermentation process liquefies the pulp, allowing it to drain away. This reduction in pulp assists the drying process. But most importantly, cocoa fermentation triggers an array of chemical changes within the bean. These chemical changes are vital to the development of the complex and much-loved flavour known as “chocolate”.

Prior to fermentation, the ripe cacao fruits (known as pods) are carefully cut from the tree. The harvested pods are taken to a central location, where the fermentation will take place. Some growers ferment their own beans in relatively small heaps on the earth floor of the plantation, while others take their pods to a co-op for larger-scale box fermentation. But regardless of the scale of the operation, the fermentation process is essentially the same.

When the pods have been gathered at the fermentary, they are broken open, and the beans are scooped out.

The men of Olboe village in Vanuatu, standing around a heap of cocoa beans which are fermenting on the forest floor. After the beans are turned, they are re-covered with banana leaves, which helps the heap to ferment evenly.

An alternative method of fermenting cocoa beans: a three-bay cacao fermentation box on Malo island, Vanuatu.

For as long as a cacao pod remains intact, its interior is sterile, meaning that it contains no yeasts or bacteria. However, during the pod-breaking and bean-scooping stage, the pulp is inoculated with wild yeasts and bacteria. Scientists have found that the bulk of these microogranisms are generally transferred from the skins of the pods to the beans, via the bean-scoopers’ hands.

In the first stage of fermentation, the wild yeasts rapidly multiply in the sweet, fruity pulp, converting the pulp’s sugar into alcohol. This initial phase takes place in the absence of oxygen – hence, it is known as anaerobic fermentation. The yeast population peaks within 24 hours.

After the yeasts have done their work, bacteria begin to take over the fermentation process, converting the alcohol into acid. This acid slowly penetrates the bean.

The bacterial phase of fermentation takes place in the presence of oxygen – hence, it is known as aerobic fermentation. This phase requires a significant amount of oxygen, so the beans are typically turned at least twice during the fermentation process, in order to introduce oxygen into the heap, and to ensure that all of the beans are fermented evenly. Typically, the beans are turned at about 48 and 72 hours after fermentation begins.

The bacteria population peaks roughly 72 hours after fermentation first begins, and decreases rapidly over the following 72 hours. Hence, the entire fermentation process typically takes about 144 hours (six days).

As well as producing alcohol and acid, the fermentation process also generates heat, typically raising the temperature of the fermenting beans to about 45 to 50 degrees Celsius (113 to 122 Fahrenheit).

  • Phase 1 (anaerobic): sugar + yeast -> alcohol + carbon dioxide + heat
  • Phase 2 (aerobic): alcohol + bacteria + oxygen -> acid + water + heat

The acid and heat generated by the fermentation kills the cocoa bean. In turn, the bean’s death causes cell walls within the bean to break down, allowing enzymes to come into contact with their substrates. These enzymes bring about some very important chemical changes within the bean, some of which are listed under points 2 and 3, below.

Enzyme: a protein that induces chemical changes in other substances. The substance that an enzyme changes is known generically as a substrate.

Very broadly speaking, three major changes happen inside the cocoa bean during fermentation:

1. Acid penetrates the bean. The acid kills the bean, lowers its pH, and produces a sour, acidic taste.
2. Bitter and astringent flavonoids are converted into milder-tasting substances. (These enzymatic processes also turn the bean from a white or purple colour, to chocolate brown.)
3. Aroma precursors are produced. These aroma precursors are later transformed into aromas, during roasting.

Below I explain these three major changes in more detail:

1. Acid penetrates the bean.

As previously mentioned, some of the acid which is produced by bacteria during the second phase of fermentation penetrates the bean. This acid is primarily acetic acid: the same acid that gives vinegar its sour taste. Most of this acid is later evaporated out of the bean, during drying and conching. However, a moderate amount of residual acidity can lend a desirable, fruity complexity to cocoa.

2. Bitter and astringent flavonoids are converted into milder-tasting substances.

Freshly harvested cocoa beans are extremely bitter, astringent, and unpalatable. This unpleasant bitterness is primarily due to high levels of water-soluble flavonoids (a.k.a antioxidants) in the bean. During fermentation, these flavonoids undergo a complex series of chemical transformations. For example:

* Some flavonoids combine with other flavonoids to produce larger molecules known as condensed tannins, or proanthocyanidins. This process is very similar to the mellowing process that fine red wine undergoes as it ages. Incidentally, proanthocyanidins are a category of antioxidants that are widely believed to be very good for you (this is why the media often hypes chocolate as a “health food”).

* In a multi-step process, some flavonoids oxidise and condense, producing the classic chocolate brown pigmentation in cocoa. This process is known generically as enzymatic browning.

During cocoa fermentation, flavonoids combine with eachother, and with proteins and amino acids, in myriad ways – not all of which are perfectly understood by science. For example:

anthocyanin [purple] + glucosidase enzymes -> anthocyanidin [purple] + sugar

anthocyanidin [purple] + polyphenol oxidase enzymes + oxygen -> quinone [yellow]

quinones [yellow] + other flavonoids + amino acids -> condensed tannins

condensed tannins + proteins -> melanin [brown, water insoluble pigment]

3. Aroma precursor development.

Freshly harvested cocoa beans taste nothing like chocolate. The bulk of the chocolate flavour-production happens during roasting, when a type of chemical reaction known as the Maillard reaction takes place. (The Maillard reaction is often confused with caramelization, which is the browning of sugar. For example, in his book, “Discover Chocolate”, Clay Gordon incorrectly states that cocoa beans are “caramelized during roasting” (p70).)

The Maillard reaction is a reaction between so-called “aroma precursors” – namely, amino acids and reducing sugars. When cocoa is roasted, the aroma precursors combine in different ways to create dozens of different flavor compounds.

These all-important aroma precursors are produced during fermentation as a result of enzyme activity. For example:

* Protease enzymes break proteins down into peptides and amino acids.

* Invertase enzymes break sucrose down into fructose and glucose. Fructose and glucose are known as “reducing sugars”


After fermentation, the cocoa beans are dried. Drying reduces the moisture content in the bean from about 55% to about 7%. With a moisture content of 7%, cocoa beans can keep for many years (in ideal storage conditions).


Notes regarding the colour of cocoa beans:

  • The cotyledons (or “flesh”) of freshly harvested cocoa beans range in colour from white to dark purple.
  • If the flesh of an unroasted cocoa bean is brown, then it has undergone enzymatic browning. (Roasting causes non-enzymatic browning, via Maillard reactions.)
  • If cocoa beans are dried without first being fermented, they become a slaty grey colour. So-called slaty beans are considered to be defective under international standards.
  • Under-fermented beans remain bright purple. This happens when fermentation is halted (by spreading the beans out to dry, for example) before the enzymatic browning processes occur. When fermentation is incomplete, the acid produced by the bacterial phase of fermentation stabilises or “fixes” the purple colour in the bean. Purple beans are far more bitter and astringent, and have fewer aroma precursors, than fully fermented beans.
  • The occurrance of slaty and purple cocoa beans is mirrored in red wine production: In red wines, acidity helps preserve and stabilize the color of the wine. More acidic wines have redder, more stable colors. Wines with higher pH (that is, less acidic wines) have higher levels of less stable blue pigments, eventually taking on a muddy grey hue. Source:

I originally published this information on The Chocolate Life forum in 2009, and that original posting attracted some great comments and questions:

Subhashini Rajasekaran asked for some pictures showing the colour of cacao beans at different stages of fermentation, which is an extremely sensible idea! So, I’ve dug out some illustrative photos for a follow-up post – coming soon.

Another request was from Jim, a Brazilian cacao grower who requested permission to use this information in his training material. For the record, I’m delighted for people to use the information I provide – in return I request acknowledgement, and (for online resources) a link to the relevant page on my website. Thanks!

And Jo (the founder of Holy Cacao chocolate) commented that “if only every person on the internet would only post information in this way, then many of the lies would disappear instead of propagate”. Thanks Jo – I couldn’t agree more.

(Frustratingly, my original post was also plagiarised – word for word – by Wiki Answers. The only parts not copied were my name as the author, and my list of references. Shame on you, Wiki Answers!)


Camu, N.; Gonzalez, A.; De Winter, T.; Van Schoor, A.; De Bruyne, K.; Vandamme, P.; Takrama, J.S.; Addo, S.K.; De Vuyst, L. (2008)
“Influence of Turning and Environmental Contamination on the Dynamics of Populations of Lactic Acid and Acetic Acid Bacteria Involved in Spontaneous Cocoa Bean Heap Fermentation in Ghana”
Applied and Environmental Microbiology, Vol. 74, No. 1, pp. 86-98

Hansen, C.E.; del Olmo, M.; Burri, C. (1998)
“Enzyme activities in cocoa beans during fermentation”
Journal of the Science of Food and Agriculture, Vol. 77, Issue 2, pp.273-281

Schwan, R.F.; (1998)
“Cocoa Fermentations Conducted with a Defined Microbial Cocktail Inoculum”
Applied and Environmental Microbiology, Vol.64 Issue 4, pp.1477-1483