Coffee cherry color: genetic, biochemical foundations and technical reading at farm level

This fact sheet aims to answer a very specific question: why do coffee varieties exist with cherries of different colors?
The answer is not found in roasting, processing, or market “trends,” but in the biology of the fruit itself: genetics, pigments, and ripening physiology.

The practical objective is to help you use color as a technical signal to:

• Define the harvest point by variety (not by a universal rule).

• Reduce the mixing of physiological states within a lot (better fermentation control).

• Make selection decisions (tree, plot, date) with traceability.

• Communicate accurately with clients (variety and phenotype) without confusing color with quality.

2. Key concept (to avoid confusion)

Cherry color is NOT a universal standard of ripeness. In many varieties, the ripe fruit is not red.
The correct interpretation is: each variety has an expected “ripe color,” and that color is explained by the pigments the plant produces—or does not produce.

At farm level, the most common mistake is treating color as a single scale (green → red), when in reality there are phenotypes where the end of the curve is yellow, pink, or orange. Without calibration, two problems arise:
(1) harvesting too late (loss of freshness, over-ripeness), or
(2) harvesting too early (physiological immaturity).

3. Where does color come from? Pigments and biochemical pathways

The visible color of the fruit results from the relative accumulation of pigments in the skin (exocarp) and, to a lesser extent, in internal tissues. In coffee, the most relevant pigments are:

• Anthocyanins (flavonoids): responsible for red, pink, and purple tones. Their synthesis depends on genes that activate the phenylpropanoid pathway.

• Carotenoids: responsible for yellow and orange tones. They are lipid-soluble and accumulate in plastids; they become more visible when anthocyanins are reduced.

• Chlorophyll: dominant in immature (green) fruits. It decreases during ripening, and its degradation allows other colors to be expressed.

In simple terms:
A red cherry usually has high anthocyanin production; a yellow cherry reduces or “switches off” part of that production, revealing carotenoids; a pink cherry expresses anthocyanins at lower concentration or in variants that shift the final tone.

3.1 Anthocyanins: why red, pink, or purple can appear

Anthocyanins are water-soluble pigments stored in vacuoles of the fruit skin cells. The final tone depends not only on how much anthocyanin is present, but also on:
(a) the specific type of anthocyanin,
(b) tissue pH,
(c) co-pigmentation with other compounds, and
(d) the cellular structure of the epidermis.

This is why two varieties with anthocyanins can end up with different colors: one deep red, another stable pink, another purple. In the field, this means the visual ripeness cue may differ even when internal physiology is similar.

3.2 Carotenoids: why yellow and orange appear

Carotenoids accumulate in lipid structures and plastids. In many varieties, they are always present but are “masked” by anthocyanin red. When the anthocyanin pathway is reduced (genetically), yellow becomes dominant. Orange usually appears when carotenoids are visible and a fraction of anthocyanins adds a warm hue.

3.3 Chlorophyll and ripening: from green to phenotype expression

In immature fruits, chlorophyll dominates and the fruit appears green. As ripening progresses, chlorophyll degrades and plastids reorganize, allowing final pigments to be expressed. If chlorophyll degradation is faster or slower (due to environment or crop load), the visual transition may change without any genetic change.

4. Fruit anatomy and where color is “seen”

The coffee cherry is a drupe. Color is observed mainly in the skin (exocarp) and can be influenced by the structure and thickness of the pulp (mesocarp).

Anatomical reminder:

• Exocarp (skin): highest pigment concentration; main visual reference.

• Mesocarp (pulp): can affect perceived color through transparency, thickness, and water content.

• Mucilage: does not define external color, but its composition and thickness vary by genetics and ripeness.

• Endocarp (parchment) and seeds: do not determine cherry color, but relate to density and processing response.

4.1 Fruit development: visible stages and complementary “signals”

For color interpretation, it helps to think in stages. While speed varies by variety and environment, a typical scheme is:

• Green stage: firm fruit, low juiciness, chlorophyll dominant, low sugar availability.

• Transition: chlorophyll degradation, sugar increase, texture changes; color moves toward its final phenotype.

• Physiological maturity: peak usable sugars, richer and more stable mucilage, juicier pulp; color stabilizes as red/yellow/pink/orange depending on variety.

• Over-ripeness: very soft pulp, higher risk of drop and damage, greater microbial colonization; color may darken or dull.

5. Cherry colors by varietal genetics (technical reading by phenotype)

Below is what each color “means” genetically and how to interpret it at harvest.
Important: color is a signal, but maturity must be confirmed with physiological indicators.

5.1 Red cherry (the most common pattern)

The most widespread phenotype in Coffea arabica, usually associated with strong anthocyanin expression at maturity. Typical progression: green → yellowish/reddish → deep red. Color-based harvesting works well when complemented with maturity checks (Brix, texture, detachment).

Typical risks:
(a) assuming darker red is “better,” when it may be over-ripe;
(b) mixing deep reds with still-firm reds in microclimates;
(c) harvesting by “red” alone without sugar sampling, leading to harsh acidity.

5.2 Yellow cherry (true yellow maturity, not immaturity)

In yellow varieties, the fruit may go from green to intense yellow without turning red, due to reduced anthocyanins. At full maturity, yellow is stable and sugar levels can be high.

Harvest reading: define a target yellow per lot (uniform golden yellow) and validate with Brix and texture. Visual variability due to shade can be high—some fruits look pale yet are ripe—so sampling is essential.

5.3 Pink cherry (pink phenotype)

In pink cherries (e.g., Pink Bourbon), anthocyanins are produced in amounts or forms that generate a pink tone. The skin may be more delicate, and in some farms higher permeability and faster fermentation kinetics are observed.

Typical risk: waiting for pink to “turn red” and harvesting late. In many pink materials, pink is the final ripe stage.
Recommendation: document the target pink visually, sample Brix, and standardize selection by tree.

5.4 Orange and purple cherries (less common)

Orange tones usually reflect a mix of visible carotenoids with some anthocyanins. Purple tones can appear due to high concentrations of specific anthocyanins and epidermal pH variation. These can be genetically stable depending on the material.

5.5 Practical cases (to ground the reading)

• Pink Bourbon: aromatic peak often occurs when pink is uniform and pulp is juicy but not soft.

• Yellow Bourbon: optimal point often appears as intense/golden yellow; pale yellows may be shade or transition—validate with Brix.

• Wush Wush: may show vivid reds and, in some materials, pink hues; selection uniformity strongly impacts cup clarity.

6. Maturity: a technical harvest protocol when color varies by variety

For technical harvesting, color must be combined with objective indicators—especially in non-red varieties.

Simple, repeatable protocol:

1. Define the target color by variety and plot (ideally with photo reference).

2. Sample 20–30 representative cherries and measure Brix (or at least assess mucilage sweetness/stickiness).

3. Evaluate pulp texture (firm, juicy, soft) and discard damaged over-ripe fruits.

4. Check detachment: ripe cherries detach with less force and without tearing tissue.

5. Separate by state (immature, target, over-ripe) and record percentages.

Alert indicators: excess soft fruits, vinegar smell in baskets, skin micro-ruptures, or high transition percentage. In these cases, reduce time between harvest and processing and adjust fermentation design.

7. Environmental influence: why the same material can look different

While genetics define color potential, the environment modulates expression.

Key factors:

• Solar radiation and shade: more radiation can intensify anthocyanins or accelerate changes.

• Temperature: affects enzymatic pathways; cool nights can enhance pigmentation.

• Nutrition (N, K, micronutrients): influences vigor, metabolism, and fruit development.

• Water and stress: deficit affects size and uniformity; excess water can dilute visual cues.

• Crop load: heavily loaded plants may show less uniform ripening.

Practical tip: if you change shade, nutrition, or crop load management, expect changes in color intensity and recalibrate the lot’s target color.

8. Relationship between color, skin, and fermentation (why it matters in processing)

Color is linked to genetic traits often accompanied by differences in skin, pulp, and mucilage, which can affect:

• Skin permeability and gas exchange (O₂/CO₂).

• Fermentation kinetics (time to mucilage breakdown, acid production).

• Risk of over-fermentation if the same time is assumed for all materials.

• Washing behavior: thinner skins are more prone to damage under rough handling.

• Aromatic potential: delicate materials require finer control (temperature, time, hygiene).

9. Record-keeping and traceability: documenting cherry color in a lot

To make color a real tool rather than a subjective comment, record:

• Variety/material and color phenotype (red, yellow, pink, etc.).

• Harvest date and time + weather conditions (sun/shade/rain).

• Selection percentage (target vs transition vs over-ripe).

• Average Brix (if measured) and texture observations.

• Photo references of the target color (same lighting when possible).

10. Quick table: cherry color and technical interpretation

11. Important note (brief): color of the hulled green bean

With prolonged fermentations or long drying, hulled green beans may show tonal changes (more yellowish, grayish, or light brown). These can relate to controlled oxidation, migration of phenolic compounds, and fermentation metabolites. This topic requires technical criteria to distinguish process variation from defects.

A future document will cover:
(1) green/hulled bean color,
(2) relationship with long fermentations and extended drying,
(3) risk signals, and
(4) how to document it with measurements.
For now, this sheet focuses on cherry color.

12. Short glossary

• Phenotype: visible expression of a trait (e.g., cherry color) resulting from genetics and environment.

• Anthocyanins: pigments responsible for red/pink/purple tones in plant tissues.

• Carotenoids: yellow/orange, lipid-soluble pigments present in many fruits.

• Physiological maturity: point at which the fruit reaches optimal internal conditions (sugars, texture, mucilage) for quality and processing.

13. Closing

Cherry color is a biological expression (genetics + physiology) and should be read as information. Used correctly, it enables more precise harvesting, more stable processing design, and a deeper understanding of varietal identity.