How coffee is made: seed to cup

Coffee passes through 31 distinct stages between a seed and a finished cup. The supply chain is not simple or uniform — it varies by country, farm size and processing choice, and can go wrong in specific, documented ways at almost every step.

Wondering how a specific choice changes flavour once you already have beans in hand? See Change the taste. This page is about what happens before that point.

On the farm: from blossom to harvest

A cherry takes many months to make, and the order in which things happen on the tree explains most of what is hard about growing and picking coffee.

The year on a coffee tree

CoffeeHQ diagram

A dry spell, then rainFlower buds wait through the dry months and open after rain returns. Rain at odd times means several flowerings.
Flowering and pollinationArabica can pollinate itself; robusta cannot, and is planted as mixtures of compatible clones.
The fruit swells, then fillsSize is set early, while the fruit expands; dry matter is laid down afterwards, while it is still green.
RipeningThe skin and pulp colour over several weeks. Fruit from different flowerings ripens at different times on one branch.
HarvestPicked ripe by hand in repeated passes, stripped in one pass, or shaken off by machine, depending mostly on slope and labour.

The sequence described in a published review of coffee physiology. Timings are in the guide to the coffee plant, with their source.

The coffee plant — Roots, flowering, pollination and the five stages of the fruit.
Where coffee grows, and why — Temperature, rain, frost and wind, and what altitude has to do with them.
Shade, spacing and water — What each choice on a farm is reported to gain and to cost.
How coffee is harvested — Four ways of picking, and why the ground decides between them.
Pests and diseases — Leaf rust, berry disease, the berry borer, wilt and nematodes.
Coffee and climate change — What is modelled, what has been observed and what is only proposed.

The seed-to-cup journey

Stage 1
Seed selection
A farmer or nursery selects healthy, ripe cherries from productive, disease-resistant trees to use as seed stock, or sources certified seed/seedlings from a research institute or government agency.
Why it matters
Genetics set a ceiling on disease resistance, yield potential and some flavour characteristics before a single tree is planted.
Who performs it
Farmers, nurseries, agricultural research institutes and seed-certification bodies.
What can go wrong
- Low genetic diversity in widely-planted varieties increases vulnerability to disease
- Uncertified seed may not match the variety it's sold as
Regional variation
Some countries have active national breeding programmes (e.g. Brazil, Colombia, Kenya); others rely more on informal farmer seed exchange.
Stage 2
Nursery
Seeds germinate and grow into seedlings in a nursery bed or nursery bags, typically under partial shade, until they are strong enough to transplant.
Why it matters
Weak or diseased seedlings at this stage carry problems into years of subsequent growth — this is the cheapest point to discard a poor plant.
Who performs it
Farmers or specialist commercial nurseries.
What can go wrong
- Fungal disease in crowded nursery beds
- Transplant shock from seedlings moved too early or too roughly
Stage 3
Planting
Seedlings are transplanted into the field at a spacing and density chosen for the farming system, often alongside shade trees in agroforestry systems.
Why it matters
Spacing, shade and soil preparation at planting affect yield, tree health and management costs for the whole of the tree's productive life.
Who performs it
Farm labourers, often under a farmer's or farm manager's direction.
What can go wrong
- Poor soil preparation leading to weak root establishment
- Erosion on steep, newly-cleared slopes
Environmental note
Land clearing for new planting is a documented driver of deforestation in some coffee-growing regions; agroforestry systems that retain native shade trees have a different environmental footprint than full-sun clearance.
Stage 4
Coffee tree development
Over several years, the young tree grows, is pruned to shape its structure, and gives little or no crop at first: a study of replanting in Central America speaks of no or very low yields for at least the first two years.
Why it matters
How a tree is pruned and maintained during this period affects its productive lifespan and long-term yield.
Who performs it
Farmers and farm labourers.
What can go wrong
- Neglected pruning leading to reduced future yield
- Nutrient deficiency from poor soil management
Regional variation
Time to first harvest and typical tree lifespan vary by variety, altitude and management intensity.
Stage 5
Flowering
Coffee trees produce small white flowers, typically triggered by rainfall after a dry period; each flower can develop into a cherry if pollinated.
Why it matters
Flowering timing and evenness determines how evenly the eventual cherries will ripen, which in turn affects how easy the harvest is to manage well.
Who performs it
A natural process; farmers may irrigate to help trigger flowering where rainfall is unreliable.
What can go wrong
- Irregular rainfall causing multiple, staggered flowering events, which spreads ripening unevenly
- Frost or heat stress damaging flowers before fruit sets
Effect on taste
Uneven flowering leads to mixed-ripeness harvests, which is one documented contributor to inconsistent cup quality — an indirect rather than a direct effect.
Stage 6
Fruit development
Fertilised flowers become small green fruit that hardly grow for the first weeks, then swell quickly, then fill with dry matter while still green.
Why it matters
Bean size is set in the weeks when the fruit is swelling, and a review of coffee physiology ties it to the rain that falls then.
Who performs it
A natural process, monitored by farmers.
What can go wrong
- Drought stress producing smaller beans
- Pest damage to developing cherries
Stage 7
Ripening
Cherries change colour (typically green to yellow to red, depending on variety) in the last stage of their growth; a review of coffee physiology says ripening on a tree can spread over about ten weeks.
Why it matters
A review of coffee physiology says a harvest with a low share of ripe cherries gives impaired beverage quality and more defective beans.
Who performs it
A natural process; farmers monitor ripening to plan harvest timing.
What can go wrong
- Uneven ripening across a tree or plot, common with irregular flowering
Effect on taste
Underripe cherries are widely associated with sour, astringent, "quaker"-type outcomes, and overripe or fermented-on-the-tree cherries with off, fermented flavours. That is the trade's account; the only source opened for it here is a physiology review that links a low share of ripe fruit to impaired quality without describing the flavours.
Stage 8
Harvesting
Ripe cherries are picked, either by selective hand-picking (returning multiple times to pick only ripe cherries), strip-picking (stripping all cherries from a branch regardless of ripeness), or mechanical harvesting on flatter, larger farms.
Why it matters
The picking method directly determines how much unripe/overripe fruit ends up mixed in, which downstream sorting can only partially correct.
Who performs it
Farm labourers, often seasonal, for hand-picking; farm-owned or contracted machinery for mechanical harvesting.
What can go wrong
- Mixed-ripeness cherries from strip-picking or a single pass
- Fallen, over-fermented fruit picked up from the ground and mixed in
- Damaged cherries from rough mechanical harvesting
Effect on taste
Selective hand-picking brings in fruit of more even ripeness, at higher labour cost, and is widely associated with higher potential cup quality. No study comparing harvest methods on cup quality was read for CoffeeHQ's harvest guide.
Regional variation
Ground a machine can drive on allows harvesters, as on much of Brazil's coffee land; a Brazilian study gives a slope of 20 per cent as the working limit for ordinary harvesters, above which fruit is taken by hand or with hand-held machines unless the rows are terraced.
Labour note
Harvest is the most labour-intensive stage of production and the point where seasonal labour shortages and wage/piece-rate conditions most directly affect farmers and workers.
Stage 9
Cherry sorting
Harvested cherries are sorted to remove unripe, overripe, damaged or foreign material, often using flotation (ripe, dense cherries sink; underripe/damaged ones float) followed by hand-sorting.
Why it matters
This is the first quality checkpoint after harvest and meaningfully affects the final lot's consistency.
Who performs it
Farm or wet-mill labourers.
What can go wrong
- Poor flotation sorting leaving too much defective material in the batch
Effect on taste
Thorough sorting reduces the proportion of underripe, overripe and damaged cherries that reach processing. No source measuring its effect on the cup was read.
Stage 10
Depulping
For washed and honey processing, a pulper machine removes the cherry's outer skin and most of the fruit pulp, leaving the bean covered in a sticky mucilage layer. Natural (dry) processing skips this step and dries the whole cherry instead.
Why it matters
Whether and how much pulp is removed is the first major branch point between processing methods.
Who performs it
Wet-mill operators.
What can go wrong
- Incorrectly calibrated pulpers damaging or cracking beans
Stage 11
Fermentation
Depulped beans (still covered in mucilage) or whole natural-process cherries are left to ferment — in tanks, open air, or sealed/anaerobic containers — so naturally occurring microbes break down sugars and mucilage.
Why it matters
International guidance gives fermentation one primary purpose in the wet process, loosening the mucilage so that it can be washed off, and treats the shortest fermentation that does so as the best one. Its length is also the choice one large trial found changed the cup most.
Who performs it
Wet-mill or processing-station operators, increasingly following deliberate, monitored recipes on specialty lots.
What can go wrong
- An unmonitored fermentation turning the coffee sour, the risk the international code of practice names
- Insufficient fermentation leaving mucilage incompletely broken down
- Contaminated fermentation water or vessels introducing off-flavours
Effect on taste
In the trials CoffeeHQ has read, a longer fermentation moved tasters' scores towards fruity and acidic notes, at one site each and by a small margin. Neither shows that longer is better.
Stage 12
Washing
For washed process, fermented beans are rinsed with water to remove the broken-down mucilage, leaving clean parchment-covered beans.
Why it matters
Washing removes the loosened mucilage so that the parchment can be dried clean. The clean, bright cup the trade expects of washed coffee is an expectation; no document CoffeeHQ has read tested it against the alternative.
Who performs it
Wet-mill operators.
What can go wrong
- Incomplete washing leaving residual mucilage that can ferment further and taint the cup
- Dirty wash water introducing contamination
Environmental note
Washing uses significant water and produces wastewater high in organic matter, requiring proper treatment to avoid local water pollution.
Stage 13
Drying
Beans (as washed parchment, honey-process beans, or whole natural cherries) are dried — on raised beds, patios, or in mechanical dryers — down to a moisture at which mould can no longer grow. The FAO guidance gives 12 per cent as the recommended maximum for parchment and 13 for dried cherry; the international code of practice gives 12.5.
Why it matters
International guidance treats drying as the stage that stabilises the crop, and time spent between wet and dry as the window in which mould can grow.
Who performs it
Farm or processing-station labourers, who rake and turn drying beds regularly.
What can go wrong
- Uneven drying leaving some beans over- and others under-dried
- Part-dried coffee getting wet again, which the guidance says may be more serious than drying slowly
- Insufficient drying leaving beans vulnerable to mould
- Rain or contamination during patio drying
Effect on taste
Slow or interrupted drying gives mould time to grow. The guidance on the subject is concerned with the toxin some moulds produce as well as with taint.
Stage 14
Resting / conditioning
Dried parchment coffee is rested for a period to let moisture stabilise evenly through the bean before milling.
Why it matters
Milling unevenly-conditioned coffee too soon can damage beans or leave inconsistent moisture that causes storage problems later.
Who performs it
Warehouse or processing-station staff.
What can go wrong
- Milling before adequate conditioning, leading to bean damage or later spoilage
Stage 15
Hulling
A hulling machine removes the dried parchment layer (washed/honey process) or the dried whole-cherry husk (natural process), exposing the green coffee bean.
Why it matters
This is the point at which coffee becomes the green bean form traded internationally.
Who performs it
Dry-mill operators.
What can go wrong
- Incorrectly calibrated hulling machinery cracking or chipping beans
Stage 16
Polishing
An optional step where a polishing machine removes the thin silverskin left on the bean after hulling, producing a smoother-looking green bean.
Why it matters
Mostly a cosmetic/market-preference step in most origins; some producers and buyers consider it unnecessary.
Who performs it
Dry-mill operators.
What can go wrong
- Over-polishing can remove more of the bean surface than intended
Regional variation
Practised in some origins and markets and not in others.
Stage 17
Grading
Green coffee is sorted by size (screen size), density, and sometimes colour, into export grades, using mechanical sizing screens and density tables, plus increasingly optical/laser sorters.
Why it matters
Grading standards and terminology differ significantly by producing country, which affects how directly grades can be compared across origins.
Who performs it
Dry-mill and export-preparation staff.
What can go wrong
- Grading errors mixing sizes/densities that behave differently in roasting
Regional variation
National systems count different things and are not interchangeable. Brazil's regulation classes coffee by type (a defect count in a 300 g sample), by screen and by cup; Kenya sorts by size and shape into lettered grades such as AA, AB and PB; Ethiopia's grades, as one study recorded them, combine defect counts with a cup assessment. See the grading guide for which documents were read.
Stage 18
Defect sorting
Green beans are inspected — by hand, mechanically, or with optical sorters — to remove defective beans (black, sour, broken, insect-damaged, foreign matter) before export.
Why it matters
Defect counts are the basis of most green-coffee grading systems. How closely a physical grade predicts the cup is less clear: CoffeeHQ has read no study testing a national grade against a tasting panel.
Who performs it
Dry-mill sorting staff, increasingly assisted by optical sorting machines on larger operations.
What can go wrong
- Manual sorting inconsistency
- Optical sorters miscalibrated for a given defect type
Stage 19
Bagging
Graded, sorted green coffee is packed into bags — traditionally jute, increasingly with a sealed inner liner or vacuum packaging for higher-value lots — for storage and shipping.
Why it matters
Packaging materially affects how well green coffee retains quality over months of storage and shipping.
Who performs it
Dry-mill or export-preparation staff.
What can go wrong
- Poor-quality or contaminated bags absorbing odours or moisture
Stage 20
Storage at origin
Bagged green coffee is held in a warehouse at origin before export, sometimes for weeks or months depending on market timing and logistics.
Why it matters
Poor warehouse conditions (heat, humidity, pests, odour sources) can degrade quality before the coffee even leaves the country of origin.
Who performs it
Exporter or cooperative warehouse staff.
What can go wrong
- Humidity causing mould
- Pest infestation
- Nearby odorous goods tainting the coffee
Stage 21
Exporting
An exporter handles contracts, quality certification, customs documentation and logistics to sell green coffee into the international market.
Why it matters
Contract terms (price basis, quality specifications, payment timing) directly affect how much of the final retail price reaches the farmer.
Who performs it
Export companies, cooperatives, or (less commonly) farms exporting directly.
What can go wrong
- Price volatility between contract and delivery
- Quality disputes at the point of sale
Livelihood effect
Farmgate price share of the final export price varies significantly by country, crop cycle and contract structure.
Stage 22
Shipping
Green coffee travels by sea (most common for bulk volumes) or occasionally air, typically in shipping containers, for weeks to reach its destination market.
Why it matters
Temperature and humidity swings during a long sea voyage can degrade quality if packaging isn't adequate.
Who performs it
Shipping and logistics companies.
What can go wrong
- Condensation inside containers ("container sweat") causing mould
- Delays extending time in transit
- Odour contamination from co-loaded cargo
Environmental note
Sea freight has a substantially lower carbon footprint per unit than air freight, which is occasionally used for urgent or very high-value lots.
Stage 23
Importing
An importer in the destination country receives, inspects, and often re-grades or samples the green coffee before selling it on to roasters.
Why it matters
Importers are often the first point where a destination-market roaster can independently verify quality against what was contracted.
Who performs it
Import/trading companies.
What can go wrong
- Quality disputes at receiving
- Customs delays
Stage 24
Green-coffee storage (destination)
Green coffee is stored by the importer or roaster in climate-controlled or at least well-ventilated warehouses until a roaster is ready to use it.
Why it matters
Green coffee's quality slowly declines over time ("ageing"), affected by temperature, humidity and how long it sits.
Who performs it
Importer or roaster warehouse staff.
What can go wrong
- High humidity/temperature accelerating quality loss
- Extended storage age flattening flavour
Stage 25
Roasting
Green coffee is heated in a roasting machine through drying, browning (Maillard reaction) and development phases, developing the aroma and flavour compounds associated with roasted coffee.
Why it matters
Roasting is where most of coffee's characteristic aroma and flavour compounds are actually created — green coffee itself smells and tastes very different from roasted coffee.
Who performs it
Roasters (from large industrial operations to small specialty roasteries).
What can go wrong
- Marks roasters call scorching or tipping, usually put down to heat applied too fast
- A roast roasters call underdeveloped
- A roast roasters call baked; two studies produced one by opposite recipes, so the word describes a result more than a cause
Effect on taste
Roasting has a large, well-documented, direct effect on flavour — see CoffeeHQ's existing roasting-basics guide for the full mechanism.
Stage 26
Degassing
Freshly roasted coffee releases carbon dioxide produced during roasting, fastest at first and then more slowly; in one study that weighed the loss, a light roast was still giving off gas a month later.
Why it matters
Very fresh coffee still holds a good deal of gas, which is the usual explanation for extra crema and uneven flow in espresso and the reason many roasters suggest resting coffee before brewing. How long is a matter of practice; no tasting study CoffeeHQ has read establishes a number of days.
Who performs it
A natural process; roasters control packaging (e.g. one-way valve bags) to manage it.
What can go wrong
- Espresso pulled very soon after roasting is commonly reported to behave unpredictably
Effect on taste
Very fresh, undegassed coffee can taste and pour differently (often with excess crema or channelling in espresso) than the same coffee a few days later.
Stage 27
Grinding
Roasted beans are ground to a size appropriate for the intended brewing method, increasing the surface area exposed to water.
Why it matters
Grind size is one of the most direct, controllable levers over extraction — see CoffeeHQ's grind-size guide and Change the Taste content.
Who performs it
The end consumer, a barista, or (for pre-ground/instant products) the producer.
What can go wrong
- Inconsistent grind (too many fines or boulders) from a poor-quality grinder
- Grinding far in advance of brewing, accelerating staleness
Effect on taste
Directly and substantially affects extraction — see the grind-size guide for the full mechanism.
Stage 28
Brewing
Hot (or cold, for cold brew) water extracts soluble compounds from the grounds using one of many methods, producing the drinkable beverage.
Why it matters
This is where CoffeeHQ's brewing-method and Change the Taste content applies in full.
Who performs it
The end consumer or a barista.
Effect on taste
See CoffeeHQ's brewing-method pages and /change-the-taste for the full detail on this stage specifically.
Stage 29
Serving
The brewed drink is served, often with milk, sugar, or other additions, at a serving temperature that itself affects perception.
Why it matters
Serving temperature and format materially change perceived sweetness, acidity and aroma.
Who performs it
The end consumer or a barista.
What can go wrong
- Served very hot, a drink can scald and is harder to taste
- Served cold, a drink is commonly said to give off less aroma
Effect on taste
Serving temperature is widely held to change how sweet and aromatic a drink seems. CoffeeHQ has not read a study of it for coffee.
Stage 30
Tasting
The drinker perceives aroma, taste and mouthfeel — a genuinely subjective step shaped by individual physiology, prior experience, and expectation, not just the coffee itself.
Why it matters
See CoffeeHQ's sensory and tasting guide for the full detail on how perception works and how to describe it usefully.
Who performs it
The end consumer.
Stage 31
Waste or reuse
Spent grounds, cherry pulp/husk (cascara), parchment and silverskin from every stage above can be discarded, composted, or put to secondary use (fuel, animal feed, cosmetics, mushroom growing, fertiliser).
Why it matters
Coffee production generates substantial organic by-product volume; how it's handled has real environmental and, increasingly, commercial implications.
Who performs it
Farms, mills, roasters, cafés and consumers, at different points in the chain.
What can go wrong
- Untreated wastewater or pulp disposal polluting local waterways
Environmental note
See CoffeeHQ's sustainability and by-products guide for the full detail on this stage specifically.

Production problems and risks

Climate, pests and disease, land pressures, and economic and infrastructure conditions all affect how much coffee gets grown, at what quality, and how well farmers are paid for it.

Climate
Rising temperatures
Average and extreme temperatures in many coffee-growing regions have risen, and are projected to keep rising — arabica in particular is sensitive to heat stress.
Effect on production
Suitability models project less land with a climate suited to arabica by the 2050s in several major producing regions, and the suitable climate moving to higher altitudes, where there is less land and much of it is steep or forested. These are projections of climate, not forecasts of what will be grown.
Effect on quality
Heat stress can disrupt flowering and uneven ripening, both associated with lower and less consistent cup quality.
Effect on livelihoods
Farmers at lower, warming altitudes are the ones the models place under most pressure; what they will do about it is not something a climate model shows.
Regional scope
The suitability studies read for the climate guide cover Latin America, East Africa and Asia; effects and the capacity to adapt vary by country.
Mitigation
Shade-tree cover (reducing peak leaf/fruit temperature and moisture loss), breeding programmes developing heat-tolerant varieties, moving cultivation to higher altitudes where land allows, and — for farmers who can access it — crop insurance and climate-index-linked financial products that pay out on defined weather triggers rather than after a full crop-loss assessment. None of these is simple or universally available: shade conversion takes years and reduces yield per hectare in the near term, breeding programmes take a decade or more to deliver widely-planted varieties, moving altitude requires land access many smallholders don't have, and insurance/finance products remain limited in reach in several producing regions.
Limitations
Long-range climate projections carry real uncertainty at the local/farm level even where the broader regional trend is well documented. Adaptation capacity itself is unevenly distributed — better-resourced farms and cooperatives can access new varieties, finance and training years before smaller, less-connected farms can.
Climate
Drought
Extended periods of insufficient rainfall stress coffee trees, particularly during flowering and fruit development.
Effect on production
Reduced yield; smaller cherry and bean size; in severe cases, tree dieback.
Effect on livelihoods
Yield loss directly reduces farm income in a crop where most producers are smallholders with limited buffer capacity.
Regional scope
The atlas's sources report it for Brazil, where the harvests of 2021 to 2025 were held down by dry spells and heat, and for Vietnam's Central Highlands in 2015-16. Severity varies year to year, and no survey of other origins was read for this card.
Mitigation
Irrigation where feasible (itself requiring capital and reliable water access many smallholders lack), drought-tolerant varieties, water-harvesting techniques (capturing and storing rainy-season runoff), mulching and cover cropping to reduce soil-moisture loss, and weather-forecasting services that help farmers time planting and interventions — access to the latter varies widely, from well-resourced cooperative-run stations to no local forecasting access at all.
Climate
Irregular rainfall
Rainfall patterns that used to be predictable enough to plan flowering and harvest around have become less consistent in several regions.
Effect on production
Disrupted or staggered flowering, leading to uneven ripening and a longer, more difficult harvest window.
Effect on quality
Mixed-ripeness harvests are harder to sort well and are associated with more inconsistent cup quality.
Regional scope
Described here in general terms; the specific pattern (too much, too little, or mistimed rain) varies by region, and no document read for this card measures it.
Limitations
Attribution of any single season's irregularity specifically to long-term climate change (versus natural year-to-year variability) requires careful, region-specific analysis.
Pest or disease
Coffee leaf rust
A fungal disease (Hemileia vastatrix) that lives only on living coffee leaves. Infected leaves fall early, and a tree stripped of leaves cannot fill its fruit.
Effect on production
A review of the disease cites yield losses of up to 35 per cent. A study of the Central American epidemic reports production down 16 per cent in the 2012-13 harvest and a further 10 per cent the year after, and notes that such figures cannot be cleanly separated from normal variation between years.
Effect on livelihoods
The same study reports falls in harvest employment and in pickers' wages during the Central American epidemic, in households that depend on that income to buy food.
Regional scope
Present in nearly all coffee-growing regions. The study of the 2008-2013 epidemics found each coincided with a period of low profitability, in which farms were tended less, and with a narrower gap between day and night temperatures.
Mitigation
In principle: resistant varieties, which the rust review calls the most effective and durable approach, though resistance can break down as new races of the fungus appear; chemical control, on which this site gives no detail because it is a matter for local agronomic advice; and keeping farms tended. Replanting with resistant varieties costs money and means at least two years with little or no crop.
Pest or disease
Coffee berry borer
A small beetle (Hypothenemus hampei). The female bores into the fruit and lays her eggs in the seed, and the larvae feed on it.
Effect on production
Direct yield loss and bean damage; considered one of the most economically significant coffee pests worldwide.
Effect on quality
Beetle-damaged beans are a recognised green-coffee defect (insect damage) that sorting aims to remove before export.
Regional scope
Present in nearly all coffee-producing countries. How many generations it completes in a year depends on temperature.
Mitigation
In principle: clearing fruit left on the tree and the ground after harvest, monitoring with traps, natural enemies, and chemical control where local advice supports it. A review of the pest notes that smallholders often cannot afford the labour that thorough clearing takes.
Pest or disease
Nematodes
Microscopic soil-dwelling worms that attack coffee roots, reducing the tree's ability to take up water and nutrients.
Effect on production
Especially damaging to newly planted seedlings; on mature trees, nutrient deficiency, leaf loss, stunting and lower yield. The symptoms above ground look like those of poor soil or drought.
Regional scope
No review of where each species matters was read. The one study read is from Kenya and says nematodes are rarely recognised there as a cause of loss.
Mitigation
In principle: starting with clean, healthy, resistant seedlings, because nematodes are extremely difficult to remove from an established planting.
Soil and land
Ageing trees and low genetic diversity
Old trees yield less, and much of the arabica grown commercially descends from a small number of plants: the published variety catalogue describes Latin American growing as still resting largely on two lines, Typica and Bourbon, which it says contributes to a genetic bottleneck.
Effect on production
Declining yields from ageing trees; low genetic diversity increases vulnerability to a disease or pest that targets a common weakness.
Effect on livelihoods
Replanting is expensive and means several unproductive years before new trees bear fruit — a real barrier for smallholders without access to finance.
Mitigation
Breeding programmes for diversity and disease resistance; financing schemes to support replanting cycles.
Soil and land
Deforestation for coffee expansion
Clearing forest land to expand coffee cultivation, historically and in some regions currently, contributes to habitat and biodiversity loss.
Effect on production
Not a production risk to existing farms directly, but an environmental cost of expansion that the atlas's sources describe for Vietnam and Peru.
Effect on livelihoods
Complex: land conversion can provide short-term income for farmers while degrading the same ecosystem services (water, pollinators) coffee farming depends on long-term.
Regional scope
The atlas's sources describe it for Vietnam's Central Highlands during the expansion of the 1990s and for parts of the Peruvian Amazon. No global figure was read, and it should not be taken as typical of coffee land in general.
Mitigation
Certification schemes with deforestation-free requirements, shade-grown/agroforestry systems that avoid full clearance.
Economic and social
Price volatility
Coffee is traded as a global commodity, and the benchmark "C market" price can swing significantly based on global supply, weather in major producing countries, and financial-market activity, largely independent of any individual farmer's costs.
Effect on production
Not a direct effect on the crop, but a major driver of whether farming coffee remains viable for smallholders.
Effect on livelihoods
A study of the leaf rust epidemics of 2008 to 2013 found that each followed a period of low profitability in which farms had been tended less. A World Bank report on Vietnam describes growers left in debt when prices fell at the start of the 2000s.
Mitigation
Fixed-price and relationship/direct-trade contracts, cooperatives with collective bargaining power, price-floor certification schemes.
Limitations
Certification and direct-trade arrangements cover only a minority of global production.
Economic and social
Low farm income and living income gaps
Many smallholder coffee farmers earn income below what researchers and NGOs define as a "living income" for their region, even in years of stable prices.
Effect on production
Chronic underinvestment in farm maintenance, fertiliser and replanting where income doesn't cover it.
Effect on livelihoods
Described by producer organisations and certifiers as a driver of rural poverty and of young people leaving farming. No study measuring that was read for this card.
Mitigation
Living-income pricing initiatives, cooperative models, diversified farm income (intercropping, agrotourism).
Limitations
"Living income" benchmarks are estimates that vary by methodology and region, not a single universally agreed figure.
Economic and social
Seasonal labour shortages
Harvest requires a large, temporary seasonal workforce; the atlas's sources report shortages of harvest workers in Brazil and in Nicaragua, where the attaché links them to emigration.
Effect on production
Delayed or incomplete harvesting, which risks over-ripening and quality loss if cherries aren't picked in time.
Effect on livelihoods
Affects both farmers (harvest risk) and seasonal workers (working conditions, pay, migration).
Mitigation
Improved wages/conditions to attract labour, mechanisation where terrain allows.
Economic and social
Limited access to finance and agronomic support
Many smallholders have limited access to affordable credit for replanting, fertiliser or equipment, and limited access to agronomic training/extension services.
Effect on production
Slower adoption of disease-resistant varieties, soil-improvement practices and climate adaptation measures.
Mitigation
Cooperative lending schemes, NGO and certification-body extension programmes, mobile agronomy advisory services.

Coffee defects

A defect is a specific, identifiable fault traceable to one stage of production. Most defects are quality issues, not safety issues — where a defect genuinely does carry a safety dimension, that's stated explicitly rather than left for a taste test to catch.

Harvest · severe
Black beans
Cause
More than one cause is named. The FAO's guidelines on mould say that too hot an air inlet in a mechanical dryer turns immature beans black. The trade more often blames over-ripe, diseased or fallen fruit; no document read for this record confirms that.
Appearance
Beans appear fully black or very dark, sometimes with a dull, brittle texture.
Sensory effect
The trade's handbook lists the possible effect of a fully black bean as highly bitter, dirty and phenolic, and classes it as a primary defect.
Prevention
Selective picking, avoiding fallen fruit, thorough flotation and hand sorting.
Harvest · severe
Sour beans
Cause
Usually attributed to over-ripe cherries or to a delay between picking and processing that lets the fruit ferment; no document read for this record confirms the cause.
Appearance
Beans may appear yellowish or reddish-brown rather than the expected green.
Sensory effect
The trade's handbook lists the possible effect of a fully sour bean as acrid, pungent, fermented and sour, and classes it as a primary defect.
Prevention
Prompt processing after harvest, careful ripeness sorting.
Harvest · moderate
Insect-damaged beans
Cause
Coffee berry borer or other pests boring into the cherry/bean.
Appearance
Small holes or tunnels visible in the bean.
Sensory effect
Can contribute musty or off flavours, and is associated with a higher risk of mould entering through the damage site.
Prevention
Integrated pest management, timely harvest of infested cherries.
Processing · moderate
Broken beans
Cause
Mechanical damage from pulping, hulling or milling equipment that is miscalibrated or poorly maintained.
Appearance
Visibly cracked, chipped or fragmented beans.
Sensory effect
Broken beans roast unevenly (more surface area exposed) and can taste burnt or ashy in the cup relative to intact beans in the same batch.
Prevention
Correct equipment calibration and maintenance.
Processing · minor
Shells
Cause
A genetic/developmental defect where an empty, shell-like husk forms alongside a normal bean in the same cherry.
Appearance
Light, hollow, curled bean fragments.
Sensory effect
Roast unevenly (often scorching) due to very low density and thin structure.
Prevention
Density-based sorting during grading removes most shells before export.
Harvest · moderate
Immature beans
Cause
Underripe cherries picked before full ripeness, often from strip-picking or a single harvest pass.
Appearance
Smaller, paler beans with a papery silverskin that clings more than on ripe beans.
Sensory effect
Described by the trade as grassy, astringent and sour. A review of coffee physiology says a harvest with a low share of ripe cherries gives an impaired beverage and more defective beans.
Prevention
Selective ripeness picking; density/colour sorting.
Roasting · moderate
Quakers
Cause
Beans that stay pale when roasted. The trade's handbook says they come from immature or drought-affected coffee and are beans with little or no grain, and that most can be removed in the washing channel.
Appearance
Visibly paler than surrounding roasted beans — the standard way roasters spot and remove them.
Sensory effect
Roasters describe a papery, peanut-like flavour if they are not removed before grinding; the handbook says only that they can affect the cup.
Prevention
Sorting green (removing immature beans) and post-roast (removing visible quakers).
Drying · severe
Mould
Safety note
Certain moulds found in poorly dried/stored coffee can produce mycotoxins (e.g. ochratoxin A), a genuine food-safety concern, not just a flavour issue. This cannot be reliably assessed by taste or smell alone — proper drying/storage practice and, where relevant, laboratory testing (not home inspection) are the appropriate controls. This is general food-safety information, not personal medical advice.
Cause
Insufficient or uneven drying, rewetting after drying, or storage in humid conditions.
Appearance
Visible white, grey or greenish fuzzy growth on beans in severe cases; may not always be visible before roasting.
Sensory effect
Musty, mouldy off-flavour.
Prevention
Thorough, even drying to correct final moisture; dry, well-ventilated storage; prompt rejection of visibly affected lots.
Processing · severe
Phenolic defect
Cause
Usually attributed to contamination during fermentation, from unclean equipment or water; no document read for this record confirms that. The trade's handbook records another route: coffee picking up a phenolic smell in a shipping container that had carried chemicals.
Appearance
Not usually visible in the green or roasted bean.
Sensory effect
Sharp, medicinal, iodine-like or "band-aid" off-flavour — one of the most severe and easily detected cupping defects.
Prevention
Clean fermentation vessels and water; controlled fermentation time/temperature.
Processing · severe
Ferment defect
Cause
Attributed by the trade to fermentation that ran too long or too warm. The trade's handbook lists a fermented sour bean among its primary defects without giving a cause.
Appearance
Not usually visible before cupping.
Sensory effect
The handbook's words for a fermented sour bean are fermented, sour and an unpleasant smell.
Prevention
Monitored, time-and-temperature-controlled fermentation.
Processing · moderate
Potato defect
Cause
Associated with coffee from the African Great Lakes region. It has been linked to the antestia bug, which damages the cherry, and to microbes that may enter through that damage; a bacterium and several fungi have each been proposed, and none is confirmed as the cause.
Appearance
Not visible before roasting or grinding.
Sensory effect
A distinctive raw-potato smell/taste in an otherwise normal-looking cup, usually noticed only after grinding or brewing a single affected bean.
Prevention
No fully reliable prevention is established; careful post-harvest handling is associated with lower incidence.
Storage or transport · minor
Baggy flavour
Cause
Green coffee absorbing odours from its sacks, from goods stored nearby or from a shipping container. The trade's handbook also records contamination from the oil used to soften jute fibre before spinning.
Appearance
Not visible.
Sensory effect
Musty, cardboard-like or "burlap" off-flavour.
Prevention
Inert inner packaging (e.g. sealed liners), clean storage away from odorous goods.
Drying · moderate
Smoke contamination
Cause
Drying coffee near open fires or in dryers using combustion sources that expose beans to smoke.
Sensory effect
Ashy, smoky taint distinct from intentional dark-roast character.
Prevention
Indirect-heat drying methods; keeping drying areas away from fires.
Storage or transport · moderate
Staleness
Cause
Oxygen, moisture, heat and light exposure over time after roasting, breaking down aromatic compounds.
Sensory effect
Flat, dull, cardboard-like flavour with little aroma.
Prevention
Airtight, dark, cool storage; buying appropriate quantities relative to how quickly they'll be used — see CoffeeHQ's storage and freshness content.
Storage or transport · moderate
Rancidity
Cause
Oxidation of coffee oils over extended time, especially in warm conditions or in pre-ground coffee with high surface area.
Sensory effect
Unpleasant, sour-fatty "off" flavour distinct from ordinary staleness.
Prevention
Cool, airtight storage and using coffee within a reasonable time of roasting/grinding.
Roasting · moderate
Scorching
Cause
Roasters attribute it to too much heat too early in the roast, marking the bean's surface before the inside has caught up. One study that produced a scorched roast deliberately did so with a very hot start.
Appearance
Dark, sometimes blistered patches on individual beans.
Sensory effect
Described by roasters as sharp, acrid and burnt.
Prevention
Roasters adjust the starting temperature and early heat for the batch size; no setting is correct in general.
Roasting · minor
Tipping
Cause
Roasters attribute it to excess heat burning the bean's pointed tip. This is craft usage; no document read for this record tests it.
Appearance
Small dark/burnt spots at the bean's tip.
Sensory effect
Described by roasters as a localised burnt flavour, usually less severe than scorching.
Prevention
Gentler heat application, especially early in the roast.
Roasting · minor
Facing
Cause
Roasters attribute it to uneven heat scorching one side of the bean. This is craft usage; no document read for this record tests it.
Appearance
A darker, burnt patch on one face of the bean.
Sensory effect
Described by roasters as a localised burnt or bitter flavour.
Prevention
Correct roaster drum rotation/airflow and batch loading.
Roasting · moderate
Baking
Cause
A roaster's word for a roast that came out flat, usually put down to too long a time at too low a heat. It names a result more than a recipe; no document read for this record fixes one.
Appearance
Dull, flat-looking bean surface.
Sensory effect
Described by roasters as flat, papery and muted.
Prevention
Roast profile with adequate heat, not just adequate time.
Roasting · moderate
Underdevelopment
Cause
A roaster's word for a roast judged to have ended too early for what was intended. It names a result; no document read for this record defines it.
Sensory effect
Described by roasters as grassy, sour or bready.
Prevention
Roasting to a defined target and tasting the result.
Roasting · moderate
Over-roasting
Cause
Roast carried well beyond what was intended.
Sensory effect
Described by roasters as burnt and ashy, with a bitterness that covers the coffee's own character.
Prevention
Roasting to a defined target profile with consistent monitoring.

How coffee is made: seed to cup

On the farm: from blossom to harvest

The year on a coffee tree

The seed-to-cup journey

Seed selection

Nursery

Planting

Coffee tree development

Flowering

Fruit development

Ripening

Harvesting

Cherry sorting

Depulping

Fermentation

Washing

Drying

Resting / conditioning

Hulling

Polishing

Grading

Defect sorting

Bagging

Storage at origin

Exporting

Shipping

Importing

Green-coffee storage (destination)

Roasting

Degassing

Grinding

Brewing

Serving

Tasting

Waste or reuse

Production problems and risks

Coffee defects

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