Armour thyroid is used to treat hypothyroidism (low thyroid hormone) and to treat or prevent goiter (enlarged thyroid gland). Because Armour thyroid is a replacement for a naturally occurring hormone, side effects do not commonly occur when thyroid hormone levels are in normal range.rmour Thyroid works by replacing the thyroid hormone when your body does not make enough on its own. It is a natural product made from animal thyroid glands (usually from pigs). There are different brands of thyroid supplements, including Westhroid, Nature-Throid, and Armour Thyroid.