Why Are My Onion Seedlings Falling Over at the Base?

Onion seedlings that suddenly collapse — falling over at the base of the stem as if the stem has been cut — have damping off. The stem at soil level turns brown, narrows to a thread, and the seedling keels over. Other nearby seedlings often follow within days. Damping off is caused by a complex of soil-borne fungi and water moulds — primarily Pythium, Rhizoctonia, and Fusarium species — that attack the tender stem tissue of seedlings at or just below the soil surface. It is one of the most common problems when raising onions (and any other vegetables) from seed indoors, and it is almost always preventable.

The conditions that cause damping off

Damping off thrives in exactly the conditions that many growers accidentally create when raising seeds indoors: warm temperatures, high humidity, stagnant air, and consistently wet compost. The causative pathogens live in compost, on containers, in tap water, and on seed surfaces. They are present almost everywhere but only become a problem when conditions tip in their favour. Covering seed trays with cling film or solid lids to retain moisture, placing trays in a warm spot without ventilation, and watering so heavily that compost stays saturated are the main triggers.

Prevention: airflow and moisture management

The most effective prevention is good airflow over the compost surface from the moment of germination. Remove any solid covers or cling film the moment seedlings emerge and keep them in a well-ventilated space — not enclosed in a propagator lid unless the lid is vented. Water from below rather than above: stand trays in a shallow tray of water for 20–30 minutes until the surface of the compost just begins to darken, then remove and allow to drain completely. Never water so heavily that water sits on the compost surface for more than a few minutes. Allow the top of the compost to dry slightly between waterings rather than keeping it constantly saturated.

Use clean, fresh compost and clean containers

Always use fresh, sterile seed compost (not garden soil or reused old compost) to start onion seeds. The pathogens causing damping off build up in old compost and can persist in dirty containers. Wash trays and modules with hot water and a mild disinfectant before reusing them. Do not use garden soil in seed trays, even mixed with compost, as it introduces a much higher pathogen load than commercial seed compost. Buying a fresh bag of fine seed compost at the start of each sowing season removes most of the pathogen risk.

Can you save an affected tray?

Once damping off takes hold it spreads rapidly and the affected seedlings cannot be saved. Remove them immediately to prevent spread. If only a small proportion of a module tray is affected, improving ventilation and reducing moisture drastically sometimes halts the spread before all seedlings are lost. Applying a light dusting of horticultural grit or vermiculite over the compost surface reduces surface humidity and can limit spread. In most cases, though, a heavily affected tray should be discarded and a fresh sowing started under better conditions.