You may experience some or none of the Armour Thyroid side effects listed in this article. Unfortunately, there is no way for your healthcare provider to know beforehand if you will have side effects from a medicine that you have never tried. Therefore, make sure to let your healthcare provider know if you develop any side effects while taking the drug or if something "just does not seem right." While it may not be a side effect of Armour Thyroid, your healthcare provider will be able to diagnose and treat the problem.