Seedlings affected by onion fly can be killed. On older plants outer leaves can yellow and wilt. The onion bulb can be destroyed as the larvae feed within it. This insect is most often encountered in central and eastern England and is most damaging during June and July.

Onion fly can be distinguished from allium leaf-miner and leek moth as it feeds on roots rather than within the leaves.

Bean seed fly can also be a problem on allium crops and can reduce seedling emergence, particularly of salad onion, dramatically.

• Encourage predators and other natural enemies in the garden such as birds, hedgehogs and ground beetles. Some ground and rove beetles are efficient predators of root feeding maggots 
• Badly damaged plants found towards the end of summer should be lifted carefully and burnt to prevent maggots from completing their development
• Some protection may be gained by using insect-proof mesh
• A mixture of pathogenic nematodes, sold as 'Fruit and Vegetable Protection', can be watered into the soil which may control the young larvae, this is available by mail order from biological control (pdf document) suppliers. They are not specific to onion fly and may also affect other insects in the soil and so should be used in a targeted manner
• Growing onions and shallots from sets, rather than seeds, can help plants to survive attacks by the first generation of larvae
• There are no insecticides available to home gardeners for controlling onion fly