When we grew onions for the first time we didn’t end up with the best results, because although this seemingly easy to grow vegetable comes in several different forms for gardeners to cultivate, choosing the right one at the very start can mean the difference between success and failure. 

The most heartbreaking moment is when your lovingly grown onions rot in storage. Once they start, it’s hard to control the spread of rot in stored onions, and it can easily spread to others causing a disaster of epic proportions.

What causes onions to rot?

After spending the year nurturing your crop to be the best they can be, the worst scenario would be rotten onions. You have a beautiful French onion soup with crusty warm bread planned for your evening meal, only to find that your cured and stored homegrown onions have gone bad. 

The cause of this is generally bacteria and fungi which will grow happily on storing onions, especially if they’re closely packed. 

There are two common causes of rotten onions in storage – Onion mushy rot, and Botrytis allii:

Mushy rot

The fungi and bacteria that can affect your onions live in the soil, so if an onion infected with mushy rot (Rhizopus microsporus) is included in your harvest for storage it can easily spread the disease to other onions if your batch doesn’t have the best airflow. 

When harvesting, signs of mushy rot can be noted by any slipping skins, or softer than normal layers on your onion. White or yellow onions will show a lacklustre appearance and look darker than their healthy neighbours, while red onions will appear almost black.

While in storage, check your onions every so often because, while early signs of infection are hard to spot, after a few weeks there will be an obvious and distinct sweet rotten smell from your harvest. Pick out any rotten smelling onions and dispose of them (don’t add them to compost as the fungus can last and infect future crops).

Botrytis allii

Botrytis is also commonly known as neck rot as this fungus that stays inactive during the growing stages is carried on the seed itself and is generally undetectable until your onions go into storage. 

You’ll only notice if Botrytis is present in your stored harvest after a couple of months, this is why it’s crucial to keep checking your store for signs of softening, especially around the neck tissue of the onion, which can then travel down into the bulb.

How to prepare onions for storage and avoid rot

There are several different problems your onions can come across in storage, and also harvest. A lot of problems during onion storage are caused by bruising or damage whilst the onions are being harvested. Just like apples, bruising on an onion can slowly develop in storage and let bacteria in. 

Once your onions have been harvested (gently!) keep that base plate of roots intact! Take care to tease out any large clumps of wet soil, any other loose soil will dry off in curing and fall out later. Harvested, prepared and stored correctly, your onions have the potential to last up to 10-12 months in storage, if not then it’ll be a matter of weeks before they spoil if left in a warm and humid environment like a kitchen.

First, make sure they have dried for long enough. Onions need an even drying temperature, most people leave onions out in the sun to dry, however, this can cause some sides of your onions to dry out more than others. Keep turning your onions gently to give them as even a drying surface as possible. A safe place for drying can be a greenhouse – just make sure it’s watertight, which ours is not! Laying your onions out separately on a dry greenhouse shelf can keep them safely away from any interruptions in their environment.

Onion growers all have their own ingenious ways of drying their crops, but the consensus is to give them good airflow, a constant temperature of 60-80°F (20-28°C), and really, just leave them alone for a few weeks.

The curing will normally take anywhere between 2-4 weeks. You’ll know when your onions have dried enough as their necks will wither and become fully papery to touch. This means that you can gently trim off the dry roots and top of the neck. Some people do leave a lot of this paper neck on as onions, much like garlic, can be displayed by hanging up, involving intricate knotting and weaving.

Finally, it’s time to put them in storage. Here’s how to store onions for safekeeping:

Best conditions for storing onions

Your onions need to be cured to create a thick outer skin before storing, as above, as this should be your onions first barrier against any bacteria or fungi infecting your crop. If this skin is thick enough it should act as a defending wall against any infections. 

However, if the papery skin is insufficient and your onions don’t have good enough airflow, the bacteria will spread more efficiently in warm, humid conditions, so let’s explore exactly what you need to do to give your onions the best chance of lasting as long as possible.

Firstly, get your growing conditions right. It’s always good to practice the best crop rotation you can for your whole vegetable garden. Making sure that you don’t plant your onions in the same place as your previous onions were growing is a good way to control any soil-borne disease spread.

Onions grown in high humidity can be more prone to fungal diseases. Keeping your onions watering routine regular but not excessive will help keep any moisture problems at bay whilst growing.

Finding a space to store onions that’s low light, low humidity and cool may be a challenge, but somewhere like a garage or spacious pantry would be perfect. Somewhere that you know you will visit regularly to keep a watchful eye over your onion harvest.

Choosing the right onions for storage

To start off with, not all onions are created equal, some varieties are better grown for storage than others so consider the suitable types before planning your vegetable garden. Generally, long-day onions like Patterson, Stuttgarter or Red Zeppelin are all excellent storing onions. Ensuring you pick the best possible onion variety will keep you well-stocked with this staple ingredient throughout the year. 

Seasoned onion growers tend to grow a selection of different varieties as even the best ‘keeper’ onions have varying storage life. Keeping onions have a thicker outer skin when cured, lower water and higher sulphur content, so chances are if it’s making you cry it’s a keeper.

Are onions grown from seeds or sets better for storage?

Onions are biennial and want to flower in their second year, so to ensure that your onion will last in dormancy (storage) grow your onions from seed, as opposed to sets, early in the year. This way, your onion bulbs will be less likely to re-sprout in storage if their conditions trigger growth. Any growth that happens in storage can make for an environment that will encourage rot.

While it’s entirely possible to store onions grown from sets, they are more likely to bolt and send out scapes (flowering stems) which will speed up rot, and make storage preparations more difficult. Growing onions from seed increases storage reliability. Growing onions from seed also increases the potential size of the onions you will harvest. 


What causes onions to rot in storage?

Onions in storage can rot if they are kept too cold, or too hot. They need cool temperatures (ideally 40-50°F) in order to store for the maximum amount of time.

Avoid storing any onions with signs of botrytis or mushy rot at the point of harvest as these can infect entire crops in storage.

Why do stored onions sprout?

Stored onions are just next year’s flowers. Given the chance, they will try their very best to send out new foliage and new flower spikes. Just like a tulip, they store their energy for next year’s flower production in their bulb, so when exposed to moisture or light they will send out shoots.

Why are my onions going mouldy?

Onions can grow mould even if you store them perfectly. It’s upsetting, but this is usually down to mistakes when we harvest them. Funguses are killed by extreme temperatures, so onions stored correctly in cool spaces can still harbour fungus if not eaten before it spreads. Always check your harvest.


Hopefully this will have helped to inform you about why your onions are rotting in storage, and some simple but effective ways to prevent this from happening by changing up some growing, harvesting and storing habits. 

Remember that it’s only the onions that you can’t eat fresh that you need to store, so if you are planning on French onion soup every night in autumn and winter, you may not have needed this article. The average person however might not be able to get away with onion breath for quite that long.

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