Why Do My Stored Onions Go Soft at the Neck?

Onions stored for two to four months that begin developing a soft, almost sunken area around the dried neck, often with grey fluffy growth visible if you look closely, have neck rot — caused by the fungus Botrytis allii. It is one of the most common and aggravating onion storage problems because it does not become visible until well into the storage period, by which time the fungus has been present for months. A store of seemingly perfect onions can lose half its contents to neck rot between October and December. Understanding how the infection works makes it entirely preventable.

How Botrytis infects the neck

Botrytis allii is airborne and infects the neck (the dried stem area above the bulb) during the final weeks before harvest, when the tops are dying back and the plant is at its most vulnerable. It also spreads through the store from affected onions to nearby sound ones via the production of grey spores visible as fuzzy growth on infected necks. The fungus requires moisture to enter — a neck that has dried hard and completely sealed itself off during curing is almost impenetrable. An incompletely dried, still slightly soft or thick neck has microscopic openings through which the fungus grows.

The critical role of curing

Curing — laying harvested onions in a single layer in a warm (20–25°C), dry, well-ventilated location for two to three weeks — is the step that prevents neck rot. During curing, the neck dries and hardens completely, cutting off the entry route for Botrytis. The outer scales dry to papery skins that further protect the inner tissue. Never rush curing. Never store an onion that still has a soft, green, or thick neck — it is not ready and will almost certainly develop neck rot. In a wet harvest season, use a greenhouse or polytunnel to complete curing indoors rather than accepting inadequately cured bulbs into storage.

Identifying neck rot before it spreads

Check stored onions every three to four weeks. Press each bulb gently just below the dried neck — sound onions resist firmly; a neck-rotted onion feels soft or spongy in that area even before external signs appear. When you find a soft one, remove it and examine it: cutting it in half will reveal the softened, usually water-soaked or brown inner tissue descending from the neck. Any onion with even mild neck rot symptoms should be used immediately — trimming away the affected area generously often leaves a usable portion. Remove the affected onion from the store promptly to prevent spread.

Other prevention measures

Avoid applying nitrogen fertiliser after midsummer — high-nitrogen plants produce thick, soft, hard-to-cure necks that are more susceptible to Botrytis. Store in cool (5–10°C), dry, well-ventilated conditions — warmth and humidity accelerate fungal spread. Store onions in nets, slatted trays, or strings rather than sealed boxes where air cannot circulate. Never store damaged, washed, or bruised onions alongside sound ones.