Jains avoid eating onions mainly because of the principle of ahimsa (non-violence) and the Jain view of cultivated life in the soil.

• Ahimsa and harm to life: Onion plants are underground in the bulb stage and harvesting the bulb typically ends the life of the plant and many small life-forms living around or inside it. To minimize harm as much as possible, many Jains refrain from root vegetables, including onions and garlic, because uprooting can kill the whole plant and disturb numerous tiny organisms in the soil.
• Purification of food for spiritual practice: Jain food rules aim to keep the eater free from violence and karmic bondage caused by unnecessary harm. Root vegetables are considered more likely to cause such harm than other vegetables, so they are often avoided.
• Differences between Digambar and Shwetambar: The core principle is the same (ahimsa), but practices vary by community. Many Shwetambar Jains follow stricter avoidance of root vegetables, while some Digambar Jains may be more flexible in certain situations; however, onions and other root vegetables are commonly avoided across both groups as a general guideline.

In short: onions are not eaten because they involve greater potential harm to living beings and because they are a root vegetable, which many Jains avoid to minimize violence and karmic impact.

For more on Jain dietary principles, see: