Why are my stored onions going soft and rotting?

Onions that rot weeks after storage were nearly always lost at lifting — neck rot, poor curing, bolted bulbs and the storage conditions that finish the job.

Difficulty: beginner
Time: 15 min
Read: 4 min

Short answer

Softness starting at the shoulder with a grey growth is neck rot, an infection carried in from the field that only shows up in store. It cannot be cured — the answer is curing the necks hard, sorting out any bulb with a thick or soft neck, and storing cool, dark, dry and airy in nets rather than bags.

Onion storage failures are frustrating because everything looked fine at harvest. That is the nature of neck rot: the infection is present at lifting, sits in the neck tissue, and only becomes visible weeks later when the bulb is in a sack in the shed. Everything you can do about it happens before the bulb goes into store.

Step by step

Work out where the rot starts.Softening at the shoulder and neck, with a dense grey mould and sometimes small black bodies, is neck rot. Softening at the base with white fluffy mould is white rot. A wet, foul-smelling collapse is bacterial soft rot, usually following damage or frost.
Sort the store immediately.Empty the whole lot out, discard anything soft, and re-store only firm bulbs in fresh nets. One rotting onion in a full net takes several with it.
Check the storage conditions.Cool, dark, dry and well ventilated. Around 0–5°C is ideal for long storage but any cool, frost-free, airy place works. A warm kitchen sprouts them; a damp shed rots them; a sealed plastic bag does both.
Use nets, trays or plaits rather than bags or boxes.Air needs to move around each bulb. Onions stacked in a solid box with no airflow sweat and rot from the middle outwards.
Cure harder next season.This is the real fix. Two to three weeks in a warm airy place until the necks are thin, dry and papery. Undercured necks are the commonest cause of a store that fails in November.
Stop watering as the tops go over.Late irrigation keeps the neck soft and green. Let the ground dry once the foliage starts to yellow.
Avoid high nitrogen late in the season.Nitrogen after midsummer produces soft, thick-necked bulbs that never seal properly. Feed early or not at all.
Never store bolted bulbs.A bolted onion has a hard flower stem running through the neck, so the neck cannot close. Use those first, fresh, within a couple of weeks.
Check the store monthly through winter.Feel each net. Removing one softening bulb early saves several others.

Tips

Onions grown from seed generally store better than those grown from sets, partly because they bolt less.
Store shallots and onions separately from potatoes — each shortens the other's life.
Heat-treated sets are worth the extra cost on a plot that bolts every year, because bolted bulbs are automatically non-storers.
Keep a written note of which variety stored well. Storage performance varies enormously between varieties and it is the most useful thing to know for next year.
A hanging net in an unheated garage or porch usually outperforms anything indoors, because the air moves.

Common mistakes

Storing in plastic bags or sealed containers — Onions respire and give off moisture. Trapped moisture condenses and the crop rots within weeks.
Storing bulbs with damaged or thick necks 'to use first' — They rot where they sit and take neighbours with them. Keep them physically separate in the kitchen.
Storing in a warm cupboard indoors — Warmth breaks dormancy. The bulbs sprout, soften and lose quality months earlier than they should.

If it doesn't work

Grey mould and softening starting at the neck, weeks into storage

Cause: Neck rot, infection carried from the growing crop — Fix: Discard affected bulbs. Prevention only: cure the necks thoroughly, buy clean sets, do not over-feed nitrogen late, and rotate the bed.

Base of the bulb rotting with white fluffy growth

Cause: White rot from the soil — Fix: Discard and do not grow alliums on that ground again. It persists in soil for 15–20 years.

Wet, slimy, foul-smelling collapse

Cause: Bacterial soft rot, usually after bruising, frost or damage at lifting — Fix: Discard immediately. Handle bulbs gently at lifting and never store damaged ones.

Bulbs sprouting green shoots rather than rotting

Cause: Store too warm — Fix: Move somewhere cooler and darker. Sprouted onions are still usable but should be eaten sooner.

Whole store failing within a few weeks

Cause: Bulbs put away before the necks were cured — Fix: Nothing to save this crop beyond eating fast. Next year extend the curing period and test each neck before storing.

Questions people ask

Can I cut the rot out and use the rest of the onion?

If the rot is a small area at the neck and the rest of the bulb is firm, dry and smells normal, you can cut generously past it and use it the same day. Discard anything soft through, slimy, foul-smelling or with mould growing into the flesh.

How long should home-grown onions keep?

Well-cured, well-stored onions of a good keeping variety commonly last from late summer through to spring. Poorly cured ones can start failing within six to eight weeks, which is the usual complaint.

Does neck rot spread from bulb to bulb in store?

It can spread to bulbs in contact with an infected one, particularly in damp conditions. That is why sorting the store and using nets rather than solid boxes matters.