Whether people who have hypothyroidism should avoid soy is a topic of debate.
Hypothyroidism is generally treated with synthetic thyroid hormone — and soy has long been thought to interfere with the body's ability to absorb the medication. However, there's no evidence that people who have hypothyroidism should avoid soy completely.
If you have hypothyroidism, take thyroid hormone replacement as directed by your doctor. Medication can be taken at any time that's best for you, and it's okay to take it on an empty stomach or with food — as long as you do the same thing every day.
Generally, it's best to wait four hours after taking thyroid medication to consume any products that contain soy. The same guidelines apply to other products that may impair the body's ability to absorb thyroid medication, including concentrated iron and calcium supplements, and antacids that contain calcium or aluminum hydroxide.