How To Detect + Treat A Hashimoto’s Flare Up Naturally

How To Detect + Treat A Hashimoto'S Flare Up Naturally Dr. Will Cole

Did you know that close to 1 in 8 women will experience a thyroid issue in her lifetime? This rate of thyroid problems has no signs of slowing down and is something I see almost daily in my telehealth functional medicine clinic. However, there is one problem that I see far more than the rest and that is Hashimoto’s disease.

This autoimmune condition can be debilitating with treatment options sadly limited in conventional medicine to medications that have their own list of side effects. In functional medicine we know there is another way. By focusing on addressing the root cause of why you feel the way that you do, we can work on healing your body naturally to put your symptoms into remission. But sometimes, flare ups do happen and symptoms can come back.

In order to address a Hashimoto’s flare up, let's first explore what Hashimoto’s is and what triggers flare ups in the first place so we can begin to heal from the inside out.


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What is Hashimoto’s disease?

Hypothyroidism - a condition where your thyroid doesn’t produce enough thyroid hormones - affects around 20 million Americans. Hashimoto’s thyroiditis is an autoimmune condition where your immune system attacks healthy thyroid cells. It is the most common cause of hypothyroidism with research estimating that up to 90 percent of all cases of hypothyroidism are autoimmune in nature.

Symptoms of a flare up

A flare up happens if you generally have your symptoms under control but they suddenly reappear leaving you feeling terrible. Flare ups can look different for every person and each flare up that you have can look different than the last with different symptoms. In general, symptoms can be similar to hypothyroidism and include:

  • Constipation
  • Fatigue
  • Weight gain
  • Brain fog
  • Poor concentration
  • Brittle hair and nails
  • Cold sensitivity
  • Muscle aches and pains
  • Anxiety or depression
  • Pale and dry skin
  • Hair loss
  • Heavy periods
  • Enlarged thyroid gland (goiter)

The amount of time that you experience a flare up can also vary depending on what triggered the flare up in the first place and the steps you are taking to calm your flare up.

Possible causes and triggers

Since everyone’s biochemistry is different, triggers are going to be unique to you with some people having a higher threshold to certain triggers than you.

1. Nutrient deficiencies

Your thyroid hormone relies on a delicate balance of key nutrients in order to function properly. Your body relies on a certain amount of specific nutrients for your immune system to function optimally. Deficiencies in selenium, (2) vitamin D, (3) and iron (4) have been linked to poor immune function in people with autoimmune thyroid conditions. 

Iodine is another nutrient that is especially important as it is needed for the production of thyroid hormones. But be aware, too much can flare up Hashimoto’s symptoms.

2. Stress

Research has confirmed the stress-thyroid connection. One study from 2001 (5) found that autoimmune thyroid patients had more stressful life events before their diagnosis, compared to control groups.

This could be due to the effect stress has on your thyroid hormone function. Your main stress hormone, cortisol, can block conversion of T4 to the active T3, and can also increase the unusable reverse T3 (rT3), further confusing the delicate balance of thyroid hormones that are so essential for good health. Many of my patients discover that their thyroid problems started after a stressful time in their lives.

3. Diet

Just like you might not be getting enough of the right nutrients, you may be eating too much of certain irritating foods. Many of my patients with Hashimoto’s find that even a small amount of gluten can flare up their symptoms with studies showing that the inflammatory effects of gluten can last up to 6 months in your body. (6)

If you are predisposed to an autoimmune condition, certain foods can cause your immune system to overreact so it’s important to pay attention to any possible food intolerances that you may have. A functional medicine practitioner can work with you to help uncover the specific foods that are contributing to inflammation in your body.

4. Toxin exposure

Our world has become increasingly toxic. Studies have shown that chemicals and heavy metals can cause an autoimmune response against the thyroid. (7)

How to treat and prevent Hashimoto’s flare ups

In mainstream medicine, you typically receive the same thyroid medication whether you have true primary hypothyroidism or an autoimmune disease attacking your thyroid, but in functional medicine we tend to treat autoimmune thyroid problems more naturally.

1. Alleviate stress

Considering stress is such a huge trigger for flare ups, it's important to alleviate stress as much as possible. Take note of what things stress you out - whether that’s relationships or situations - and limit your participation to avoid a potential flare up. If you are in the middle of a flare up, add in mindfulness practices like meditation and deep breathing exercises to actively lower your cortisol levels.

2. Add in supplements

If you know you are deficient in certain nutrients it might be time to consider supplementation. While I believe food is foundational, sometimes supplements can be helpful when pushing to overcome any deficiencies.

3. Try an elimination diet

If you are unsure what foods are causing your flare ups, an elimination diet is a great tool that you can use to find out what foods are optimal for your body. By eliminating a specific set of foods most likely to cause inflammation and slowly reintroducing them one at a time, you’ll be able to see what foods your body loves and what foods are better kept off your grocery list.

4. Switch to non-toxic products

If you are trying to avoid a flare up or put your symptoms into remission, switching to non toxic products - particularly beauty and personal care products as these are absorbed directly into your skin - is going to help lower your toxin load, chronic inflammation, and detoxification pathways.

5. Avoid added iodine

As I mentioned earlier, iodine is necessary for thyroid hormone production. However, it is very easy to go overboard if you have Hashimoto’s disease. Avoid products fortified with iodine like table salt and opt instead for Himalayan pink sea salt.

Consulting a functional medicine professional

If you are tired of living with symptoms or side effects of your medication, let me be the first to say that you are not alone and there is hope for healing. A Hashimoto’s flare up can be discouraging but once you know what triggers your symptoms you can make a plan to avoid flare ups and overcome them if they do occur.

In my telehealth functional medicine clinic we work with you to run more comprehensive thyroid labs with narrower reference ranges to get to the root cause of your thyroid problems, identify your triggers, and make a plan for long-term sustainable healing.

If you are ready to take that next step, consider a telehealth consultation to learn more about how we can help your Hashimoto’s symptoms with functional medicine.

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe.


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  1. Nobuyuki Amino 4 Autoimmunity and hypothyroidism Bailiére's Clinical Endocrinology and Metabolism Volume 2, Issue 3 August 1988. doi:10.1016/S0950-351X(88)80055-7
  2. Roland Gärtner, Barbara C. H. Gasnier, Johannes W. Dietrich, Bjarne Krebs, Matthias W. A. Angstwurm, Selenium Supplementation in Patients with Autoimmune Thyroiditis Decreases Thyroid Peroxidase Antibodies Concentrations, The Journal of Clinical Endocrinology & Metabolism, Volume 87, Issue 4, 1 April 2002, Pages 1687–1691,
  3. Baeke, Femke et al. “Vitamin D: modulator of the immune system.” Current opinion in pharmacology vol. 10,4 (2010): 482-96. doi:10.1016/j.coph.2010.04.001
  4. Zimmermann, Michael B, and Josef Köhrle. “The impact of iron and selenium deficiencies on iodine and thyroid metabolism: biochemistry and relevance to public health.” Thyroid : official journal of the American Thyroid Association vol. 12,10 (2002): 867-78. doi:10.1089/105072502761016494
  5. Matos-Santos, A., Nobre, E.L., Costa, J.G.E., Nogueira, P.J., Macedo, A., Galvão-Teles, A. and De Castro, J.J. (2001), Relationship between the number and impact of stressful life events and the onset of Graves' disease and toxic nodular goitre★. Clinical Endocrinology, 55: 15-19.
  6. Mainardi, Elsa et al. “Thyroid-related autoantibodies and celiac disease: a role for a gluten-free diet?.” Journal of clinical gastroenterology vol. 35,3 (2002): 245-8. doi:10.1097/00004836-200209000-00009
  7. Langer, Pavel et al. “Fish from industrially polluted freshwater as the main source of organochlorinated pollutants and increased frequency of thyroid disorders and dysglycemia.” Chemosphere vol. 67,9 (2007): S379-85. doi:10.1016/j.chemosphere.2006.05.132

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Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, The Inflammation Spectrum and the brand new book Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.

Gut Feelings Dr. Will Cole 6

Gut Feelings

Healing The Shame-Fueled Relationship
Between What You Eat And How You Feel