Hashimoto’s Thyroiditis - Part Two
Managing Hashimoto’s – A Personalised, Functional Approach
As I outlined in part 1 of this blog, managing Hashimoto’s should not be just about replacing the thyroid hormone as the gland production fails. In fact, in my extensive clinical experience with the condition, I see many clients who never need medication at all. My aim in clinic is to introduce key dietary and lifestyle strategies that can restore calm and appropriate function to the immune system, and, identify and remove the triggers or mediating factors that are fuelling the condition.
A case of mistaken identity
One well-researched theory suggests that the immune dysfunction in Hashimoto’s thyroiditis can be triggered or worsened by certain environmental factors – particularly dietary proteins like gluten.
Molecular mimicry is when a foreign substance, like a virus, bacteria, or even a food protein such as gluten, resembles the body’s own tissues. In Hashimoto’s, certain gluten proteins or microbial antigens (found on the surface of organisms like viruses and bacteria) may look similar to thyroid proteins like thyroid peroxidase (TPO) or thyroglobulin. As a result, the immune system, while trying to attack the invader, may mistakenly target the thyroid. This mistaken identity can trigger the autoimmune response, making molecular mimicry the spark that confuses the immune system into attacking the body’s own tissue (1).
Then a process called “cross-reactivity” further compounds this issue. In individuals with compromised gut integrity or '“leaky gut”, undigested food proteins, including gluten and other structurally similar molecules from dairy, soy, or certain grains, can enter the bloodstream. In those already sensitised to gluten, the immune system may begin reacting to these other proteins as well. In some cases, these reactions extend to thyroid-specific structures such as thyroglobulin or thyroid peroxidase. The immune system may then produce antibodies not just against gluten, but also against the body’s own thyroid tissue. This is particularly relevant in Hashimoto’s, where anti-TPO and anti-thyroglobulin antibodies are commonly found. As a result, ongoing gluten exposure in sensitive individuals may perpetuate thyroid autoimmunity through this cycle of immunological confusion (2). While not everyone with Hashimoto’s is gluten-sensitive, research and clinical observation have led many practitioners, like me, to recommend a strict gluten-free diet. In those with positive gluten-related antibodies or coexisting Coeliac disease it is a crucial first step to healing (3).
Adopting a gluten-free diet can lead to noticeable improvements for many but not all and many of my clients gain:
Reduced Inflammation - Eliminating gluten may help lower systemic inflammation, especially in people with gluten sensitivity or Coeliac disease, which can ease autoimmune activity.
Improved Thyroid Antibody Levels - Some people see a reduction in thyroid antibodies (like anti-TPO and anti- thyroglobulin) when gluten is removed, signalling a decrease in immune system attack on the thyroid.
Better Gut Health - Gluten can increase intestinal permeability (“leaky gut”) in sensitive individuals. Healing the gut may reduce immune system overactivation and improve nutrient absorption.
More Stable Energy Levels - Many people with Hashimoto’s report feeling less fatigued and more mentally clear once they eliminate gluten.
Improved Nutrient Absorption - A healthier gut can lead to better absorption of key thyroid-supportive nutrients like iodine, selenium, zinc, and iron.
Reduced Bloating and Digestive Issues - If gluten causes digestive symptoms (like gas, bloating, or diarrhoea), cutting it out may relieve those issues and improve overall well-being.
Balanced Immune Response - Removing a potential trigger may help calm an overactive immune system and slow progression of autoimmune thyroid damage.
Potential Weight Stabilisation - Some people experience easier weight management when inflammation decreases and metabolism stabilises.
Improved Skin and Hair Health - As the autoimmune response calms, symptoms like dry skin and hair loss may improve.
Less Brain Fog - People often report clearer thinking and improved focus after going gluten- free, especially if gluten was contributing to immune reactivity (4,5)
For some individuals, eliminating dairy and soy may provide additional benefits, as these foods can also trigger immune responses and inflammation in those with autoimmune tendencies (6). It is important that we assess food sensitivities on an individual basis.
In addition to removing reactive foods like gluten and dairy and soy where necessary, addressing broader aspects of gut health is crucial in managing Hashimoto’s. As I mentioned above, the integrity of the gut lining plays a significant role in immune regulation. A “leaky gut” or increased intestinal permeability allows undigested food particles, toxins, and microbes to pass into the bloodstream, triggering systemic inflammation and immune responses. This not only contributes to autoimmune flare-ups but can also worsen thyroid dysfunction over time. Supporting the gut barrier with nutrients like L-glutamine, zinc, and collagen, along with anti- inflammatory foods and targeted probiotics, can help restore balance (7). Identifying and addressing chronic infections too is yet another important part of the puzzle and gut connection. I regularly find H. pylori (8), candida (9), parasites (10), or SIBO (11), when I test gut function and these are known persistent immune triggers driving the condition for many.
Additionally, gut microbiome diversity is essential. An imbalance of gut bacteria - known as dysbiosis - has been linked to autoimmune conditions, including Hashimoto’s (12). Beneficial microbes help regulate immune function, support digestion, and maintain the mucosal barrier. Regular intake of fermented foods (like sauerkraut or kefir, if tolerated), prebiotic fibres, and high-quality probiotics can improve microbial balance.
Furthermore, viral infections, particularly Epstein-Barr virus (EBV), have been strongly linked to the development and progression of Hashimoto’s thyroiditis (13). EBV, the virus responsible for Glandular fever, can remain dormant in the body and reactivate during times of stress or immune suppression. Research suggests that EBV may trigger autoimmunity, again through molecular mimicry, where viral proteins resemble thyroid tissue, leading the immune system to attack the thyroid. EBV has also been found in the thyroid tissue of some patients with Hashimoto’s, indicating it may play a direct role in thyroid inflammation.
Managing viral load and supporting the immune system are key strategies in cases where chronic viral activity is suspected alongside a comprehensive gut-healing approach if I suspect involvement of either/both.
“Canary in the coal mine” – the toxin link
We also know that toxins play a significant role in the development of Hashimoto’s disease. The thyroid gland is highly sensitive to toxins because it acts as a receptor for many substances in the body, especially heavy metals and environmental pollutants. Toxins like pesticides, mercury, and flame retardants have been shown to disrupt thyroid function and contribute to the development of autoimmune thyroid disease. As these toxins accumulate in our environment, it’s no surprise that the prevalence of Hashimoto’s has been on the rise (14).
The thyroid is essentially the canary in the coal mine for many environmental stressors. When the body is exposed to these toxins, the immune system may mistake them for threats, leading to an autoimmune response that targets the thyroid. As these toxins disrupt the thyroid’s ability to produce and regulate hormones, they not only worsen the condition but also accelerate the damage to thyroid tissue. This connection between toxin exposure and autoimmune thyroid conditions highlights the growing need to be more mindful of our environment and, the chemicals we are exposed to daily (15, 16).
Part of this goal should be to optimize our detoxification abilities. Toxins act as physical stressors and are a significant burden to our body. Detoxifying the body and reducing harmful chemical exposure can significantly help in managing symptoms and slowing disease progression. The thyroid’s vulnerability to toxins, combined with its role as a receptor for many harmful substances, makes it even more critical to prioritize a clean, toxin-free lifestyle in the management of Hashimoto’s and optimize detoxification ability via:
Increased hydration
Increased sweating with exercise & sauna therapy, lymph drainage
Increased liver support with key herbs and nutrients
Lower alcohol and caffeine intake
Castor oil packs and more
The adrenal link
In addition to lowering physical stressors on the body, it is imperative to lower emotional or personal stress too. Adrenal and thyroid health are hugely connected and, while the intricate link is too big to detail here, it is well established that a high adrenal burden, from chronic levels of personal stress, can increase inflammation and worsen autoimmune conditions like Hashimoto’s (17).
Effective stress management strategies might include:
Mindfulness and meditation –can help lower cortisol and improve immune function.
Breathwork – Techniques like deep diaphragmatic breathing can help regulate the nervous system.
Gentle exercise – Walking, yoga, or Pilates can reduce stress without overburdening an already fatigued system.
Adequate sleep – Prioritising sleep is essential, as poor rest can worsen fatigue and inflammation.
Reducing stimulants – Excess caffeine and sugar can stress the adrenal glands and worsen energy crashes and burden the adrenals.
Red light therapy – early research shows a potential benefit for Hashimoto’s thyroiditis in combination with selenium and vitamin D supplementation (18).
Supporting stress resilience through lifestyle changes, adaptogenic herbs, mindfulness practices, and proper sleep is a key component in managing Hashimoto’s and promoting long-term thyroid balance.
To sum up, chronic stress or stressors can be emotional, physical or environmental and all can play a significant role in the development and progression of Hashimoto’s.
Beyond diet
While food should always be the first source of nutrients for anyone and a cornerstone strategy in any autoimmune condition, some targeted supplementation can be helpful when true deficiencies exist. I tend to test first, and common depletions I see, include: selenium, vitamin D, iron, magnesium and some key B vitamins. All of these are critical to thyroid function (18).
Selenium – Protects the thyroid from oxidative damage and helps lower thyroid antibodies. Found in Brazil nuts, eggs, and fish.
Zinc – Supports immune regulation and thyroid hormone conversion (of the inactive hormone thyroxine (T4) to the active hormone, triiodothyronine (T3) in the peripheral tissue). Found in shellfish, pumpkin seeds, and beef.
Vitamin D – Plays a critical role in immune function and inflammation control. Many with Hashimoto’s are deficient. Best obtained from sunlight and supplementation if levels are low.
Iron – Essential for thyroid hormone synthesis. Low levels (even without full anaemia) can worsen fatigue and hair loss. Found in red meat, spinach, and lentils.
Magnesium – Helps regulate stress and muscle function. Found in leafy greens, nuts, and seeds.
B vitamins – Particularly B12, which supports energy production and nerve function. Found in animal products and fortified foods.
Detective work
Hashimoto’s is a complex and increasingly common condition, and what works for one person may not work for another. My job is to help you uncover your root causes, mediating factors and address these in a systematic and targeted way to lower antibodies, halt the attack and restore immune balance.
Functional testing is a very useful tool to help guide our strategy and uncover underlying imbalances that may be driving the autoimmune activity and might include:
Blood work: to assess thyroid antibodies such as anti-TPO and anti-thyroglobulin, as well as TSH, free T3, and free T4 to fully assess thyroid function. Also, I use blood testing to investigate nutrient deficiencies, inflammation and food sensitivities.
Stool/Breath testing - to assess for SIBO, gut dysbiosis, yeast and parasite overgrowths, inflammation and igA immune response
Urine testing – to assess oxidative stress, nutrient deficiencies, mineral imbalance, detoxification issues, heavy metal or mould exposure.
Salivary hormone testing – to provide insights into adrenal health by measuring cortisol levels throughout the day, helping to assess stress response patterns that may be contributing to fatigue, poor recovery, and hormone imbalance
Work with me?
Through my personal experience of reversing elevated thyroid antibodies and restoring thyroid function, I’ve developed a strong foundation in evidence-based, root-cause approaches to managing Hashimoto’s thyroiditis. This journey has informed my clinical practice and deepened my commitment to supporting individuals in identifying their unique triggers, optimizing immune function, and improving thyroid health. At Pom Nutrition, I offer a personalised and integrative approach, grounded in current research and functional medicine principles, to guide you through every step of your healing process.
Academic References:
1. Molecular Mimicry and Autoimmune Thyroid Disease.
2. Antibody Cross-Reactivity in Autoimmune Disease.
5. The Role of Gluten in the Development of Autoimmune Thyroid Disease: A Narrative Review.
6. Thyroid, Diet, and Alternative Approaches.
7. Supporting Healthy Intestinal Permeability With the Use of Collagen.
9. Chronic Mucocutaneous Candidiasis Associated With Hypothyroidism: A Distinct Syndrome.
10. Wentz, I. Is Blasto Behind Your Hashimoto’s, Hives, and IBS?
11. Association Between Hypothyroidism and Small Intestinal Bacterial Overgrowth.
12. Gut Microbiota and Hashimoto’s Thyroiditis.
13. A Possible Link Between Epstein–Barr Virus and Autoimmune Thyroid Disorders.
14. The Pathogenesis of Hashimoto’s Thyroiditis: Further Developments in Our Understanding.
15. The Effects of Environmental Synthetic Chemicals on Thyroid Function.
16. Environmental Exposures and Autoimmune Thyroid Disease.
17. Stress Management in Women With Hashimoto’s Thyroiditis: A Randomized Controlled Trial.