Coffee: Fermentation — Wet and Anaerobic Processing

Fermentation has always been an implicit step in coffee processing — even traditional washed processing relies on microbial activity to degrade the sticky mucilage layer surrounding coffee parchment. What has changed in modern specialty coffee is the intentionality: producers are increasingly treating fermentation as a precision tool to develop specific flavor compounds, applying the vocabulary and techniques of winemaking and craft brewing to coffee.

Microbial Community Overview

Coffee fermentation is driven by a succession of microbial communities that shift as substrate composition, pH, and oxygen availability change over time:

Fermentation Phase	Dominant Organisms	Primary Metabolites	Duration
Initial (aerobic, high pH)	Enterobacteriaceae, wild yeasts	CO₂, initial mucilage breakdown	0–6 hours
Mid-phase (aerobic, pH dropping)	Saccharomyces cerevisiae, Pichia spp.	Ethanol, CO₂, esters	6–24 hours
Late phase (low O₂, low pH)	Lactic acid bacteria (Leuconostoc, Lactobacillus)	Lactic acid, acetic acid	12–48+ hours
Over-fermentation (if extended)	Acetic acid bacteria, spoilage microbes	Acetic acid, butyric acid	>48h in warm climates

The succession from aerobic yeast activity toward lactic acid bacteria mirrors patterns seen in other fermented foods (sourdough, kimchi, wine). The final pH of a properly fermented washed lot typically falls between 3.8–4.5 — low enough to inhibit spoilage organisms and signal complete mucilage degradation.

Traditional Wet Fermentation

In conventional washed processing, depulped coffee parchment is placed in open concrete or tile-lined tanks, submerged in water (or fermented dry, without added water, as is common in some African origins). Naturally occurring microbes on the cherry surface, in the water, and in the environment inoculate the fermentation.

The process is monitored primarily by tactile assessment: trained mill workers periodically reach into the tank and rub handfuls of parchment between their palms. When the fermentation is complete, the mucilage has been fully enzymatically and microbially degraded, and the parchment surface feels clean and slightly rough — no longer slippery. At this point, the tank is drained and the parchment washed with multiple changes of clean water.

Temperature is the most important variable. At lowland temperatures (25–30°C), a well-loaded tank may complete fermentation in 12–24 hours. At highland altitudes where night temperatures fall to 12–15°C, the same process may require 48–72 hours. In warm, overloaded, or poorly managed tanks, fermentation can tip into over-fermentation within 24–36 hours, producing vinegary, harsh, acetic defects — a primary reason for cup quality failures in improperly monitored wet mills.

Key Microbial Species

Research by Pereira et al. (2014) and Masoud et al. (2004) using culture-independent molecular methods has characterized the microbial ecology of coffee fermentation in detail:

• Saccharomyces cerevisiae: The primary fermenting yeast in coffee, as in wine and beer. Produces ethanol and CO₂ as it metabolizes mucilage sugars; also produces aromatic esters that contribute positively to cup character in moderate amounts.
• Pichia fermentans and Candida parapsilosis: Common non-Saccharomyces yeasts in coffee fermentation; contribute to aromatic complexity through production of higher alcohols and esters.
• Leuconostoc mesenteroides and Lactobacillus plantarum: Dominant lactic acid bacteria in the mid-to-late fermentation stage. Produce lactic acid that contributes perceived brightness and a clean, round acidity to the final cup.
• Enterobacter spp.: Present in early fermentation phases; their populations decline as pH drops. Some Enterobacter species produce negative flavor compounds; their early elimination by declining pH is a normal and beneficial outcome.

Anaerobic Fermentation

Anaerobic processing represents a deliberate departure from the traditional aerobic fermentation environment. Depulped parchment coffee (or sometimes whole cherries) is loaded into sealed food-grade tanks — typically stainless steel or high-density polyethylene with one-way CO₂ relief valves. The tanks are sealed immediately after loading, purging atmospheric oxygen as the resident microbes consume it and generate CO₂.

The absence of oxygen changes the microbial metabolic pathway fundamentally. Aerobic respiration gives way to anaerobic fermentation: yeasts undergo alcoholic fermentation, but more importantly, lactic acid bacteria (which thrive in low-oxygen, low-pH environments) come to dominate the community and produce lactic acid as the primary fermentation end product rather than acetic acid.

Flavor outcomes are distinctive and often dramatic: lactic acidity has a softer, creamier character than acetic; the combination of lactic acid, longer fermentation esters, and CO₂ dissolution creates flavor profiles that tasters frequently describe as passion fruit, cinnamon, tropical candy, or fermented grape — notes absent in conventional washed coffees.

Process Variables in Anaerobic Fermentation

Variable	Effect on Flavor
Temperature	Lower (15–20°C) → slower fermentation, more lactic, cleaner; higher (25–30°C) → faster, more volatile, higher defect risk
Duration	Longer → more lactic acid accumulation, more aromatic compound development; too long → over-fermentation defects
pH endpoint	Typically 4.0–4.5; below 3.8 risks extreme sourness
Wild vs selected yeasts	Selected (commercial) yeasts → more consistent, predictable; wild → higher complexity variance
Whole cherry vs depulped	Whole cherry anaerobic → more mucilage substrate, higher sugar, more intense fermentation flavor
CO₂ injection	Some producers inject CO₂ at the start to purge oxygen faster, accelerating the shift to anaerobic conditions

Quality and Consistency Considerations

Fermentation is the highest-risk processing step in terms of cup quality. Unlike mechanical processing steps with clear physical outcomes, fermentation is a biological process sensitive to temperature, microbiome composition, substrate chemistry, and timing. Small variations between batches — even from the same farm — can produce meaningfully different cup profiles.

Consistent fermentation requires monitoring of time, temperature, and pH, and sensory assessment at multiple stages. In the specialty coffee industry, producers who have mastered fermentation control are able to replicate distinctive flavor profiles across harvests, turning a source of variance into a reliable quality signature. For exporters and buyers, fermentation documentation (time, temperature, pH logs) is increasingly requested as part of traceability records.