Can a toddler who drinks soy milk every night have an allergy of coughing?

Yes: Drinking soy milk does not protect you from developing allergies to other things, and he could have environmental allergies that are causing the cough. Make sure environment is clear of allergens - dust and clean his room, get rid of stuffed animals, no sleeping with pets, etc. Also, do not ever expose him to second hand smoke. If symptoms of cough persist, you need to see his doc for further eval.

Yes and it might not: Be related to the soy .My ? Would be: how old is the baby? Are you using soy because you suspect allergy? Or just out of choice? How long has coughing been going on? Just @ night? Daytime too? Awakens the baby?..Try to think about all of these things then speak to your pediatrician or a board certified allergist. Also, how soon before the baby goes to bed are you giving bottle? Try it earlier.