Why Is My Onion Bulb Rotting in the Ground?

Onion plants that wilt, yellow, and collapse — and when pulled reveal a rotten, disintegrating bulb at the base — have a soil-borne disease at the root. Several distinct pathogens cause bulb rot in the ground, and identifying which one you have matters because the persistence in soil, and therefore the rotation length needed, varies enormously between them. Here is how to tell the main causes apart and what each means for your garden.

Fusarium basal rot

Fusarium oxysporum f. sp. cepae causes a dry, brown rot starting at the basal plate (the root-plate at the bottom of the bulb) that progresses inward through the scales. The outer skin is initially intact but the base feels soft and the roots are rotted. In humid conditions, white to pink fungal growth may be visible on the rotted base. Plants pull out of the ground easily because the roots have failed. Fusarium is most active in warm soil (above 15°C) and is most common in summer. There is no chemical treatment available to home growers. Rotation to a different bed every three to four years and removing all crop debris reduces build-up.

White rot

White rot (Sclerotinia cepivorum) is the most serious and persistent onion disease because its sclerotia — tiny black resting bodies — survive in the soil for 20 years or more without a host. White rot causes a similar collar rot and foliage collapse but is diagnosed by the dense white fluffy mycelium at the bulb base, studded with tiny black sclerotia. The white cotton-wool-like growth is unmistakeable. If you see it, the disease is in your soil and will affect all alliums — onions, garlic, leeks, shallots — for decades. Remove all affected plants and as much surrounding soil as possible. Do not grow any alliums in that area for as long as practically feasible.

Bacterial soft rot

Bacterial soft rot (Pectobacterium or Dickeya species) causes a wet, slimy collapse of bulb tissue with a very strong, unpleasant odour. It enters through wounds from pests, mechanical damage, or any soft tissue, and thrives in warm, wet conditions. Unlike fungal rots, bacterial soft rot often affects individual plants scattered across the bed rather than spreading in a cluster from an initial focus. Damaged sets planted in waterlogged ground are the most common source. Good drainage, careful handling, and using undamaged sets significantly reduce risk.

What to do at harvest

When you find bulb rot in your onion bed, harvest the whole crop immediately rather than leaving remaining plants to deteriorate. Sort ruthlessly — any bulb with soft, discoloured, or foul-smelling tissue should be used immediately or discarded. Sound bulbs can be stored normally. Remove all rotted plant material from the site and do not add it to compost. For white rot, treat the soil as contaminated for any future allium crop and plan rotation accordingly.