Yes, they can do pooja, but in Jainism eating roots is not considered proper ahimsa acharan.

Simple understanding:

• Bhakti and devotion are allowed for everyone.
• But a Jain should strive to avoid root vegetables like onion, garlic, potato, etc., because they involve harm to living beings.
• So, a person who eats roots may still pray, bow, and do bhav pooja, but they should understand that this habit is against Jain discipline.

Better Jain practice:

• Give up root vegetables.
• Keep body and mind pure for pooja.
• Perform pooja with shraddha, vinay, and ahimsa.

In short: