Crops

Onion black mould: where it comes from, how to assess a batch

Onion black mould is the fungus Aspergillus niger. We explain how to spot it, what favours it, how we prevent it and how to assess a mouldy batch on receipt.

Agro-Malz TeamSeptember 25, 20268 min read
Loose yellow onions in a tall pile in our storage facility

Onion black mould is a disease caused by the fungus Aspergillus niger, which leaves a black, powdery growth at the neck and under the outer skins. Onions usually pick it up in the field and at harvest, and the disease develops in warmth and moisture. What decides a batch's fate, then, is how quickly the onion dries and cools down after harvest. Below we describe how to recognise black mould, what favours it, how we prevent it and how to assess a mouldy batch on receipt.

How to recognise black mould on an onion

The most telling sign is black, soot-like clusters of spores. They appear at the neck and on the outer, dry skins, often in streaks along the skin's veins. Affected skins look water-soaked at first. Sometimes the inside of the onion is already discoloured, even though nothing shows from the outside.

At an advanced stage, the fungus moves down into the fleshy scales, and secondary wet bacterial rot takes over the onion. A bulb like that goes soft and stops being sellable.

Black mould is easy to confuse with other storage diseases. The simplest way to tell them apart is by the colour of the growth and where the problem starts:

DiseaseCauseWhat you seeWhere it starts
Black mouldAspergillus nigerblack, powdery growth in streaks under the dry skinneck and outer skins
Neck rota fungus of the genus Botrytissoftening from the neck, grey mould under the skinneck, top to bottom
Fusarium basal rotFusarium oxysporum f. sp. cepae and Fusarium proliferatumrot from the base, white mycelium on the basal platebasal plate, bottom to top

We write about the other two diseases separately in our posts on onion neck rot and onion fusarium basal rot.

Where black mould comes from

Aspergillus niger lives on plant debris and in the soil, and its spores travel on the air. It is a weak pathogen: it usually does not attack healthy, undamaged onions. It gets in through wounds, bruises and the neck while the leaves are drying down.

To develop, it needs two things at once:

  • Warmth. It grows best at 28-34°C. According to Purdue University's extension service, the disease shows up most often when the temperature in the field goes above 30°C, or above 24°C in storage.
  • Water on the surface of the onion. According to the University of California's IPM programme (UC IPM), an onion has to stay wet for at least 6-12 hours for infection to take hold.

That gives the typical scenario: a hot harvest, onions bruised during loading, and then temperature swings that cause water to condense on the skin and between the layers. The USDA's storage handbook (Agriculture Handbook 66) states this directly: infection usually starts in the field, and after harvest the disease can spread from onion to onion, which is why the surface of the onion has to be dry during and after harvest. We explain where water on a cold onion comes from in our post on why onions sweat.

How we prevent black mould

Protection against black mould rests on growing practice and post-harvest conditions, not on chemicals. We grow onions under the principles of Integrated Plant Production, so above all we make sure the fungus gets neither a wound nor water.

  1. We harvest in two stages. A Grimme WV 180 windrower undercuts the onions and lays them in windrows to cure, and a self-propelled AVR Puma 3 harvester picks them up from the windrows. The neck has time to close before the onion reaches the trailer. We describe how we limit bruising in our post on mechanical damage at harvest.
  2. We cure for 2-4 days. Airflow through the pile draws water off the surface of the onion and closes the neck. That is how we take away the moisture the fungus needs to infect. Details in our post on curing onions.
  3. We cool and hold a stable temperature. Below around 15°C, black mould practically stops developing, and cool storage at moderate humidity slows its spread. In our 13 000 tonne store, we make sure the temperature does not swing, because every swing is a risk of dew on the skin.
  4. We sort optically. The DOWNS CropVision optical sorter scans onions at 360 degrees and rejects bulbs with visible defects. Growth hidden under dry skin is not always visible from the outside, which is why quality control of a batch does not end at the sorter.

Cold stops black mould, but it does not kill it. If onions from an affected batch reach a warm, humid warehouse, the fungus starts again. That is why conditions after delivery matter just as much as our own conditions.

A red machine undercutting onions and laying them in a windrow in the field
Onions cure in windrows before reaching the trailer. A dry neck means fewer places for the fungus to get in.

How to assess a mouldy batch on receipt

Neither the UNECE FFV-25 standard nor the EU general marketing standard name black mould specifically. It is assessed through the minimum requirements: onions have to be sound and clean, and produce showing signs of rotting or deterioration that make it unfit for consumption is excluded. In Class I, the UNECE standard allows at most 1 percent of bulbs that are rotten or fail the minimum requirements; in Class II, at most 2 percent. We write more about the classes and tolerances in our post on onion quality classes.

In practice, what matters is how deep the growth reaches. It is worth cutting a share of the bulbs from the sample and assessing them like this:

What you see in the sampleHow to read itWhat to do
A few black streaks on the outer, dry skin; fleshy scales clean and firma visual defect, not deteriorationcount the share in the sample and check it against the class in the order
Growth under successive skins, fleshy scales discolouredinfection is progressingset those bulbs aside and report them to the supplier with a description of the scale
The onion is soft, wet and has an unpleasant smellsecondary bacterial rotcount it as a rotten bulb, within the tolerance for rot
Growth appeared after a few days in the receiver's warehousewarmth and condensation after deliverycheck the warehouse's temperature and humidity

If the scale of the growth exceeds the tolerance, it is worth filing a complaint straight away, with photographs of the cross-sections and the batch marking. We describe how to do that and how we handle it in our post on vegetable batch complaints.

Can an onion with black growth be eaten?

Some strains of Aspergillus niger can produce mycotoxins under laboratory conditions: fumonisins and ochratoxin A. There is very little data on their levels in onions themselves. In one study of 40 onion samples from Saudi Arabia, fumonisin B2 was detected in 37.5 percent of samples, and ochratoxin was not detected.

We have not found official guidance that addresses onions directly. The US food safety agency, USDA FSIS, gives a general rule for firm vegetables with dense flesh, such as cabbage or peppers: cut away at least 2.5 cm around and below the mould, and discard soft, moist produce whole. FSIS does not address onions, and an onion is built of layers the fungus can travel between more deeply, so this is only an inference by analogy.

Because infection can be invisible from the outside, it is worth cutting open an onion with visible growth. If the growth is only on the dry skin, and the fleshy scales underneath are clean and firm, we peel off the affected skins with a margin. If the growth or discolouration reaches the fleshy scales, or the onion has gone soft, it is better to throw it out.

Onions from Żuławy, straight from the grower

We grow around 250 ha of onions in Żuławy, harvest them with our own machines, cure them and store them in our own facility. That means we know the conditions every batch was held under before it reaches you. We describe how we grow, from sowing to harvest, in our guide onions from Żuławy: how we grow them. For our offer, take a look at onions from Żuławy, and send your enquiry through the contact form. We calculate the price based on current market rates.

Frequently asked questions

It is a disease caused by the fungus Aspergillus niger. It shows up as a black, powdery growth at the neck and between the outer skins, often in streaks along the skin's veins. At an advanced stage it reaches the fleshy scales and leads to secondary rot.

Infection usually starts in the field, but after harvest the disease can spread from onion to onion. It develops in warmth and with water on the skin. Below around 15°C it practically stops, though cold does not kill it.

Some strains of this fungus can produce mycotoxins, and there is little data on their levels in onions. Infection can be invisible from the outside, so it is worth cutting open an onion with growth on it. If the growth is only on the dry skin, we peel it off with a margin. If it reaches the fleshy scales or the onion has gone soft, it is better to throw it out.

Yes, if the scale of the defect in the sample exceeds the tolerance in the standard or the order. The UNECE FFV-25 standard allows at most 1 percent rotten bulbs in Class I, and at most 2 percent in Class II. A few streaks on dry skin are assessed as a visual defect, not deterioration.

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Author: Agro-Malz Team

Published: September 25, 2026

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