Biochemistry and Physical Changes in Cacao Beans During Fermentation

Biochemistry and Physical Changes in Cacao Beans During Fermentation

By Ingrit Jaimes — Microbiologist, M.Sc. & Chocolatier

Fermentation is the most critical step in transforming raw cacao beans into fine chocolate. During this process, sugars in the mucilage are broken down into acids, alcohols, and heat, triggering a cascade of biochemical and physical transformations that define the flavour, aroma, and overall quality of the final chocolate.

Proper fermentation enhances chocolate’s complexity, reduces bitterness, and develops the floral, fruity, and nutty notes that define fine cacao. Unfermented or poorly fermented beans lack true chocolate character and can compromise the final product’s quality.

1. Importance of Proper Fermentation

The quality of the cacao beans depends on several factors:

• Pod maturity: fully ripe fruits yield the best beans.
• Pod health: diseased or damaged fruits negatively affect flavour and fermentation.
• Varietal characteristics and local environment: fermentation protocols differ by region, climate, and variety.

Each farm should develop its own fermentation protocol according to its specific conditions, variety, and post-harvest infrastructure. The goal is consistency, flavour development, and the elimination of off-notes or defects.

2. Theobroma cacao Varieties

There are three principal genetic groups of Theobroma cacao, each with distinct sensory and fermentation characteristics:

• Criollo — fine-flavour cacao, mild acidity, delicate floral and nutty notes. It typically ferments in about 5 days and is more sensitive to temperature fluctuations.
• Forastero — robust and high-yielding, stronger and more bitter flavour. Requires 6–7 days of fermentation for optimal flavour development.
• Trinitario — a natural hybrid of Criollo and Forastero, offering a balance between flavour and resilience. It ferments in 5–6 days and is common in premium chocolate production.

3. Biochemical and Physical Changes During Fermentation

Day 0–1: The Beginning — Anaerobic Phase

After the beans are extracted from the pods, they remain surrounded by a sugary white pulp called mucilage, which has a natural °Brix level between 10–20, though I have occasionally found values above 30 °Brix, which is unusually high.

Personally, I love the flavour of the mucilage — for me, it’s similar to soursop (guanábana), sweet and tangy with tropical notes.

• Beans are placed in wooden boxes or rotating drums.
• During the first 24–48 hours, the environment is anaerobic, with very little oxygen.
• Yeasts convert the sugars into ethanol (alcohol) and release heat.
• The temperature begins to rise, and the pulp starts to liquefy and drain naturally.
• No movement or mixing occurs during this stage — the mass is left still to allow yeast activity to dominate.

Day 1–2: Transition Phase

• The pulp continues to break down and flow out of the mass.
• The temperature rises toward 40–45 °C.
• The beans begin to swell internally; their cell structure loosens, and the outer mucilage layer becomes thinner.
• The first visible colour changes appear — from pale beige to light brown or reddish tones.
• This transition prepares the beans for oxidation and acid diffusion.

Day 3–4: Aerobic Phase — Acetic and Lactic Acid Formation

• The mass is turned or transferred to another box (ladder-style systems) to introduce oxygen.
• Acetic acid bacteria oxidize ethanol into acetic acid, while lactic acid bacteria produce lactic acid, increasing acidity and temperature.
• Internal temperatures reach 45–50 °C, sometimes slightly higher in large fermentations.
• These acids penetrate the beans, killing the embryo and initiating enzymatic reactions that generate flavour precursors — amino acids, peptides, and reducing sugars.
• The beans darken internally, showing brown or reddish-brown streaks, a key indicator of fermentation progress.

Day 6–7: Final Oxidation and Aroma Development

• The microbial activity declines, and enzymatic oxidation of polyphenols becomes dominant.
• This oxidation reduces bitterness and astringency, transforming the colour into deep brown or red-brown.
• The beans become looser in structure, easier to break and later roast.
• Properly fermented beans dry and roast uniformly, while poorly fermented (flat, purple, or unripe) beans lead to harsh, earthy, or rubbery flavours during roasting.
• At this stage, the chocolate aroma begins to emerge — the soul of cacao starts to express itself.

A high-quality batch should contain at least 70% fully fermented beans, with the remaining 30% partially fermented, contributing fruity and floral nuances that enrich complexity.

4. The Cut Test

The cut test is one of the simplest and most reliable methods to evaluate fermentation progress and bean quality.

• A sample of 50–100 beans is cut lengthwise.
• The internal colour and texture reveal the degree of fermentation and any defects.
• Well-fermented beans: brown to reddish-brown, uniform colour, distinct internal streaks.
• Partially fermented beans: purple or marbled tones, still firm.
• Defective beans: grey, black, or moldy, often indicating poor fermentation or improper drying.

5. Drying and Moisture Control

Even after perfect fermentation, poor drying can destroy cacao quality. The goal is to remove moisture gradually and evenly while preserving flavour precursors.

Sun Drying — Casa Elba System

• Beans are dried on sliding trays (“Elba”) that can be covered during rain or at night.
• On the first day, avoid direct sunlight so the shell does not harden prematurely — trapped internal moisture leads to mold growth.
• Continuous mixing and air circulation are essential.
• The final moisture content should be below 7% to ensure proper drying and prevent mold development.
• When drying is too fast or uneven, beans stick together and lose their desirable flavour profile.

Alternative Drying Systems

• Elba trays on rails or movable covers
• Camilla drying beds
• Marquesina (greenhouse-type)
• Rotary or mechanical dryers for high-volume consistency

6. Infrastructure and Materials

The fermentation system must retain heat while allowing controlled airflow.

• Wooden boxes: traditional and ideal for artisanal production. Must be made from non-aromatic hardwoods, thick and resistant, to avoid imparting unwanted scents.
• Rotary drums: provide efficient, uniform mixing.
• Controlled fermentation centres: use insulation or double walls to maintain stable temperatures, especially in colder regions.
• In Colombia, most bean extraction is manual, and by-products like mucilage and placenta are repurposed for animal feed or plant-based sub-products.

7. Evaluating Final Quality

A well-fermented cacao bean shows:

• Loose structure and slight swelling
• Uniform brown internal colour
• Dead embryo (essential for flavour development)
• Non-sticky shells after drying
• Clean aroma — fruity, floral, slightly acidic, with no mold or earthy odours

When properly fermented and dried, the beans are ready for roasting, where the chemical precursors formed during fermentation evolve into the deep chocolate aromas we know and love.

8. The Art and Science of Fermentation

Fermentation is both a science and an art. It combines microbiology, chemistry, and centuries of farmer wisdom. Each day and each movement inside the fermentation box shape the future of the chocolate bar.

A well-controlled fermentation ensures:

• Balanced acidity and complex aroma
• Reduced bitterness and astringency
• Uniform roasting and winnowing performance
• Chocolate with depth, texture, and personality

“The aroma of great chocolate begins not in the factory, but in the fermentation box — where nature, time, and care work together.” I.J.

At Artilate

At Artilate, we approach cacao fermentation as both science and art. Every batch is monitored through strict quality controls — from °Brix and temperature tracking to detailed cut tests — ensuring our chocolates capture the authentic flavour and aroma of well-fermented cacao. Our exhaustive quality controls guarantee that every bean expresses its best character — from fermentation to the final chocolate.