Black Mold On Onions

A few weeks ago I decided to harvest all of my onions, as the tops were all dead, and I wanted to clean the garden bed out. I put them in a basket and sat them on a shelf in my kitchen.

Black Mold On Onion

Yesterday, I was making dinner and the recipe called for onions. Oh good, I’ve got some of those! I pulled them out and began peeling back their flaky outer dry scales or layers.

As I prepped them for the cutting board, I began to notice that every one of the onions I had peeled had this black stuff on it, underneath the skin. I figured it was just dirt, no big deal, so I washed it off and kept peeling more onions.

I was about to start chopping the onions up, when I started to wonder about those black spots. I wasn’t so sure it was just dirt. I mean, if it was dirt, why was it underneath the layers and not simply on the surface?

I quickly discovered what it really was: Aspergillus Black Mold.

This is a pretty common fungus among home-grown onions in particular. It comes from the onions getting too hot or humid while being stored.

Fortunately, there are a few easy ways to identify, prevent, and address black mold on onions if you happen to detect it. The good news? You can usually still eat the onions, too!

What is Black Mold of Onion?

Black mold on onions is a disease caused by one pathogen – a fungus named Aspergillus niger. This pathogen lives in the soil and is very common. Here, it feeds on dead plant tissue.

While this is the most common way that black mold is introduced to onions, it’s also important to note that this pathogen can be seed borne.

The spores can be found everywhere, including in the air and soil. More often than not, plants are infected when they are wounded, either on the bulb tissue, the roots, or most commonly, the neck tissue. This occurs when the onion matures and the top begins to fall over – a telltale sign that the onion is mature.

The black that you will see on the exterior of the onion is spores and mycelium, which often is produced along veins and creates vertical streaks on the bulbs.

Sometimes, the black growth is visible even before you move the outer scales of the onion. It can also be found in the neck tissue. As the mold spreads, the entire onion bulb will get black discoloration and the onion will shrivel up.

This spread can occur both prior to harvest as well as in storage. It can happen to onions stored in the refrigerator and can contaminate nearby food.

Black mold occurs at ideal temperatures between 59 and 93 degrees F (15 C to 33 F). Although black mold won’t grow in extremely warm temperatures (above 116 degrees) it won’t grow when the onion is very cold, either.

Like most fungal diseases, black mold favors humid conditions. When the relative humidity is higher than 81%, black mold can appear in as little as three hours.

Although it sounds like it would take extremely humid conditions to produce this kind of mold growth, the reality is that this often happens in the field.

Summertime temperature fluctuations and unpredictable irrigation or precipitation can raise humidity, as can the process of curing onions. When onions are cooled rapidly, they can sweat, which obviously increases humidity, too.

What are the External Symptoms of Black Mold on Onions?

If black mold is threatening your onion crop, it will be pretty obvious that this is at play.

You’ll usually see the infection at the neck tissues first, usually once the foliage has started to dieback as the onion matures.

The infected bulbs might appear to be blackened around the neck, and any affected scales will start to shrivel up.

Later, you’ll see masses of large, powdery spores (these too are black) that look streaky along the veins of the onions as well as between exterior dry scales. The infection can advance from the neck into other flesh scales of the onion.

As the disease becomes more advanced, the whole bulb will turn back and secondary infections may make their way to the onion. Bacterial soft rot is common, which usually causes the whole bulb to get mushy and soft.

Prevention of Mold on Onions

There are a few ways you can prevent black mold from appearing on your onion crop.

Plant Healthy Seed

It’s not always possible to know the quality of the seed you are planting but do your best to plant disease-free and disease-resistant seedstock.

If you’re saving your own seed, store them in cool, dry conditions where they can’t be contaminated by other plants or seeds.

Choose Storage Varieties of Onions

Consider growing cultivars that are known for their excellent storage capabilities. That way, you won’t have to worry about them spoiling in storage before you get the chance to eat them.

Some good options to consider include:

  • Cortland
  • Talon
  • Red CreolePontiac
  • Patterson
  • Yellow Globe
  • Yellow Sweet Spanish
  • White Sweet Spanish
  • Red Bull
  • Southport White Globe
  • Stuttgarter
  • Brunswick
  • Copra
  • Red Wind
  • Bridger

If you don’t choose one of these, look for an onion variety that has a thicker outer skin and lower water content. A higher sulfur content is also a good indicator of an onion that will store well. How do you know that it has high sulfur? It makes you cry when you’re cutting it!

Be Careful During Harvest

When you’re pulling your onions in front of the field, be careful about how you handle them. Don’t bruise the bulbs while you’re handling them and don’t toss them into crates – bruising can increase the likelihood of mold appearing.

Even bruises or injuries that you can’t see – those that are invisible to the naked eye – can create entry points of the disease. Be as careful as possible and consider wearing gloves while you’re harvesting and handling your onions.

Control Foliar Diseases

Although mold can arise seemingly out of nowhere, some studies suggest that it’s more likely to form when the onions are already affected by some other disease.

Foliar diseases weaken the plant and make it harder for your onions to ward off fungal infections, such as black mold.

Time Your Harvest

Time your harvest time as accurately as possible. Harvesting your onions as soon as they are ready to be pulled will help reduce the likelihood of humidity and temperature fluctuations leading to fungal diseases in the field.

If you can, try to plan your plantings and harvests so that the onions are out of the field before temperatures get extremely hot in the latter portion of the summer. Black mold is most common where onions are grown under warm conditions, such as the hotter portion of California.

Rotate and Space Out Crops

Black mold can affect all kinds of crops, but you should do your best to rotate out similar crops within the same family so that you aren’t planting the same group in the same spot year after year.

Don’t plant onions where onions were the year before. Also, avoid planting onions where things like garlic or chives were grown in years past, since this, too, can increase the likelihood of black mold. Space your onions out in the garden from similar plants in the same family (like garlic) to make sure the mold doesn’t spread to other bulbs.

Dry Bulbs After Harvest

Once you’ve harvested your onions, get them inside to dry as soon as possible. Don’t heat the onions – heated air can increase the likelihood of black mold – but instead just make sure you keep them in a cool, dry area to cure.

Store Properly

Keep your onions stored in the right conditions. Not all onions are suitable for long term storage, but those that are should be kept at low temperatures of around 34 to 59 degrees Fahrenheit (1 C to 15 C). They also need to be kept in as little humidity as possible.

Like most fungal diseases, black mold proliferates best when the conditions are warm and damp. By running a dehumidifier where you are storing your onions or taking other measures to control the humidity, you can prevent the spread of black mold.

If you store in a location besides somewhere like a root cellar or basement, consider storing your onions in the refrigerator. This can slow mold growth and the onions will last there for around two months.

Clean the Garden Up

After harvest, don’t leave waste there to rot. Although this fertilizes and replenishes the soil, A. niger is most abundant on rotting plant material. You can’t totally get rid of fungal diseases by cleaning up the garden, but removing old plant matter can help prevent additional problems.

Remove all waste and compost it (or feed it to your chickens). Ensure that there is good drainage in the field to prevent the mold from developing next year.

Can You Eat Onions With Black Mold?

If you’ve noticed black mold on onions that you have in storage, you might be wondering whether it’s safe to eat.

The answer? It really depends. Food safety experts are mixed on this one. The microorganisms that feed on raw plants are not usually pathogenic to humans but occasionally, you could have a reaction. You should avoid eating onions if you have a known mold or Aspergillus allergy.

That said, onions have many layers, so most of the time, you can cut around the piece that’s affected, especially if there’s only small amounts of the black mold. It’s only if the mold penetrates through the entire onion that you should throw the whole thing out. You can peel off any of the affected layers and cut an inch around the black portion.

If you’re really worried, cut the affected piece out and wash the entire remaining onion with a teaspoon of vinegar mixed with a few cups of warm tap water. This should take care of any contamination and the unaffected part of the onion will be safe to eat (especially if you cook it afterward).

If you do happen to notice black mold developing on the onions that you have in storage, eat the damaged ones up first. They won’t store as well, and the sooner you get rid of them, the better – that way, they won’t continue to affect other onions that you have stored.

Otherwise, know that it’s totally safe to eat onions with a bit of mold on them, as long as they aren’t severely moldy to the point of turning soft.

Prevent Black Mold on Onions in the Future

The best way to reduce the likelihood of black mold affecting your onion crop or storage supply? Minimize injury, both before and after you have harvested your crops. Also, be sure you are storing your onions in the right conditions.

When you store onions, you should keep them at 34 to 59 degrees Fahrenheit and in low humidity.

At the end of the day, I probably should have done something different to prevent black mold from being a problem on my onions.

Maybe I should have stored them in the fridge? I definitely should have allowed them to dry well before storing though.

It was really hard throwing away all of my onions. I was so tempted to just wash them off and use them! *Sigh* But of course, it wasn’t worth the risk of making my family sick. Oh well. At least the pig enjoyed them!

black mold on onions pin image

last update: 12/06/2021 by Rebekah Pierce

16 thoughts on “Black Mold On Onions”

  1. There’s no reason to throw them out. Do not waste good food. Just peel and wash. No one will get sick because of it.

    I’m a Chef.

  2. I’ve found black mold on my onions from the store. It was not only in the layers, but the center. After reading this, I knew I had to just toss them. Shame though, the family likes onions with their tacos. I didn’t want to risk anyone getting sick though..

  3. We use mildly molded onions anyways; but they can go fast once the mold starts. I toss the outer layers, wash thoroughly… and honestly, I tend to cook onions for a very long period anyways: things like spaghetti sauce and the onions thicken it up nicely.

    Onions are one of my best crops here in the low desert of CA. They like sandy poorer soil with good drainage. Not alot of humus or manure. I don’t plant them after grass or wheat, as it tends to encourage the molds. Fresh manure is not good for them. Wait at least a year after applying manure, if you can, before planting onions. Side dressings of Blood meal and bone meal are much better. They need enough nitrogen to get healthy leaves, which result in large bulbing later; but too much and the plants get disease. They really are a great desert crop for that reason.

    I dry mine a few days (or up to a week) above grade, leaves and all atop the dry garden bed. Then I lay them out in layers on old nursery flats and move them to air dry some more in the garden shed, sheltered from direct light and moisture. Once the necks are fully cured and dry, I know it’s safe to put them in crates (like milk ones that let air through) and store in my dry garage. They will keep for at least three months for me that way. Some will even store many months more; but some sprout, some mold (and must be used or tossed immediately or it spreads). I go through the boxes every few weeks to cull out those. Dixondale Farms in TX has a great website and explains it all pretty well. I often buy their onion plants to save on the water necessary to germinate the onions in the summer months; since onions are my winter crop here. I plant sometime after the first rains in Nov, up until mid January. Harvest is sometime in June. Nature decides that one. I begin culling out around Easter, so I can get bigger onions in June, and so we can begin enjoying the harvest.

    Your climate is different from mine; but this may give you an idea of how to grow them better. Oh… as I cull, I make a few extra big spots and insert watermelon or butternut squash seeds or plants. I find the rotation works well. I’ve tried planting with lettuce and it works, but the onions seem to suffer a bit. But if I’m short on space I’ll do it anyways. They seem to do well following my yard long pole beans; but sometimes I’m too lazy to pull out the trellis.

  4. I always put my onions (and potatoes) on a big blanket/sheet/etc and leave them in the sun for a few days. I’ve had some mold problems, but it’s mostly in the spring after they’ve been in the basement all winter. I don’t think you store them in the fridge. I would recommend that you go to the library and check out some books on storing food, canning, etc. Don’t reinvent the wheel all the time – use the knowledge others have gained through the years.

    • Susan,

      I figured the fridge was a good idea ’cause everything I read suggested that the onions be stored between 34* and 40*. BUT, from what I’ve read since posting this it seems that the problem was more that I didn’t allow them to dry properly before storing. Carla Emery (Encyclopedia of Country Living) suggests that the onions be set in the sunshine for three days or so before bringing them in; then storing them in a cool, dry place in a cardboard box.

  5. Hmmm, that’s interesting because we just peel that layer off and continue to use the onion. That’s what my grandfather always did and he was a life long farmer. We’ve never been sick and I’ve never made my family sick by doing this. My pap always said that stuff was only on the first layer and it didn’t mean the whole onion was bad. I guess I’ve never given it a second thought! But this is also coming from a woman that lets her kids lick the brownie batter spoon! Ha!!

    • Tabatha,

      Really? See, that’s totally what my first inclination was to do. It was only the first layers. I hated to toss the rest of the “good” part away. After reading more about this mold, it doesn’t seem that it’s very toxic, even when exposed. You might get a headache or something, but it’s not going to kill you. Hmmm… I guess if things get bad enough we will take the risk and just eat the good parts. For now, life didn’t depend on those onions, so it wasn’t complete tragedy losing them. Thanks for the info though! It’s good to hear advice from those who’ve done otherwise.

  6. I’m with Tabitha on this one, I just peel that layer off, wash and use the onion, we’ve never been sick or had any problems.

    Tabitha, I lick the brownie batter spoon too!!!


  7. This has happened to me before as well. After all that hard work growing them and then you have to throw them out. But I’m glad the pig enjoyed them. 🙂

  8. When I harvest onions, I tie them up in bundles and hang them from the rafter on the porch of the garden shed. They’re out of the rain and direct sun, have plenty of air circulating and dry very quickly. And it’s sort of pretty 🙂 We’ve had lots of 90 degree weather and high humidity this month, but so far, no mold!


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