Healing from hypothyroidism and Hashimoto’s thyroiditis requires more than just medication. For many, the key to symptom relief and immune balance lies in the food they eat every day. From a functional medicine perspective, nutrition is foundational to reversing thyroid dysfunction, calming autoimmunity, and supporting whole-body healing.
This article explores the best dietary approaches for those living with hypothyroidism and Hashimoto’s, with a focus on Autoimmune Paleo (AIP), Paleo, and Gluten-Free diets. Each is rooted in functional medicine’s goal of identifying and removing inflammatory triggers, nourishing the body with whole foods, and restoring balance across all systems.
Why Diet Matters in Thyroid Health
The thyroid gland is highly sensitive to inflammation, nutrient deficiencies, and gut imbalances—many of which are driven by dietary choices. In Hashimoto’s, an autoimmune condition, the immune system mistakenly attacks the thyroid. Food sensitivities, blood sugar instability, and poor gut health can worsen this immune response.
Supporting the thyroid through diet involves:
- Reducing inflammation
- Healing the gut lining
- Balancing blood sugar
- Providing essential nutrients for hormone production and conversion
Autoimmune Paleo (AIP) Diet
What Is the AIP Diet?
The Autoimmune Protocol (AIP) is an advanced version of the Paleo diet that focuses specifically on calming autoimmune activity. It eliminates the most common inflammatory and immune-reactive foods for a period of time, then reintroduces them carefully based on the body’s response.
Foods Eliminated on AIP
- Gluten, grains, legumes, and dairy
- Nightshades (tomatoes, peppers, eggplant, white potatoes)
- Eggs and nuts/seeds (initially)
- Refined sugar, industrial seed oils, and processed foods
- Alcohol and caffeine
Foods Included
- Organic vegetables (except nightshades)
- Pasture-raised meats and wild-caught fish
- Organ meats and bone broth
- Fermented foods (if tolerated)
- Healthy fats like olive oil, coconut oil, and avocado
- Fresh herbs and healing spices (non-nightshade)
Benefits for Thyroid and Autoimmune Health
The AIP diet can:
- Reduce thyroid antibody levels
- Improve gut permeability (“leaky gut”)
- Lower systemic inflammation
- Support immune regulation
- Alleviate symptoms such as joint pain, fatigue, bloating, and brain fog
Considerations
AIP is restrictive at first and best followed under the guidance of a practitioner. After symptoms improve and inflammation is reduced, foods are gradually reintroduced to identify personal triggers.
Paleo Diet
What Is the Paleo Diet?
The Paleo diet mimics what early humans ate—whole, unprocessed foods that were available before agriculture. It eliminates foods that are difficult to digest, inflammatory, or disrupt the gut and hormones.
Foods Eliminated
- Grains (wheat, corn, rice, oats)
- Legumes (beans, peanuts, soy)
- Dairy
- Refined sugar and processed foods
- Industrial seed oils (canola, soybean, corn)
Foods Included
- Grass-fed meats and wild fish
- Eggs
- Vegetables and fruits
- Nuts and seeds
- Healthy fats like olive oil, coconut, and avocado
Benefits for Thyroid Health
The Paleo diet:
- Supports nutrient density and reduces food triggers
- Helps stabilize blood sugar and reduce insulin resistance
- Improves gut health and microbiome diversity
- Reduces inflammation and oxidative stress
- May assist with weight management and energy levels
When It’s Most Effective
Paleo can be a sustainable long-term option for many thyroid patients. It’s less restrictive than AIP and ideal for those who do not have significant autoimmunity or severe digestive symptoms.
Gluten-Free Diet
Why Go Gluten-Free?
Gluten, a protein found in wheat, barley, and rye, is a known immune trigger for individuals with Hashimoto’s. Studies show that gluten may mimic thyroid tissue, potentially triggering or worsening autoimmune attacks through a process called molecular mimicry.
In those with celiac disease or non-celiac gluten sensitivity, gluten can increase gut permeability (leaky gut), leading to further immune dysfunction and nutrient malabsorption.
Benefits of Going Gluten-Free
- May reduce Anti-TPO and Anti-TG antibodies
- Supports intestinal healing
- Improves absorption of critical thyroid nutrients like selenium and iron
- Reduces fatigue, brain fog, and bloating
How to Implement
Going gluten-free involves avoiding:
- Bread, pasta, baked goods made from wheat, barley, rye
- Hidden gluten sources in sauces, soups, and processed foods
- Cross-contamination from shared cooking surfaces
Choose naturally gluten-free foods like:
- Vegetables, fruits, legumes (if tolerated)
- Rice, quinoa, buckwheat, cassava, and other gluten-free grains
- Fresh meats and fish
- Gluten-free flours and baked goods (used sparingly)
Nutritional Support for Thyroid Healing
Key Nutrients to Include
Regardless of which dietary template is followed, thyroid health depends on:
- Selenium – lowers antibodies and supports T4 to T3 conversion
- Zinc – necessary for hormone production and immune function
- Iron – supports TPO enzyme and oxygen delivery
- Magnesium – regulates stress and energy production
- Vitamin D – modulates immune response
- Omega-3s – reduce inflammation
Functional Support with Foods
- Brazil nuts (selenium)
- Oysters and pumpkin seeds (zinc)
- Liver and grass-fed beef (iron and B vitamins)
- Leafy greens and almonds (magnesium)
- Wild salmon and sardines (omega-3s)
- Mushrooms and sun exposure (vitamin D)
Mind-Body Connection in Nutritional Healing
Healing from thyroid disease also means slowing down, becoming more conscious about what and how we eat. The thyroid, governed by the throat chakra, is deeply connected to our voice, self-expression, and sense of truth.
From a functional medicine lens, food should not only be nourishing—it should be:
- Eaten mindfully, in a relaxed environment
- Chosen with intention, not out of fear or restriction
- Aligned with your emotional and spiritual healing process
Conclusion
There is no perfect one-size-fits-all thyroid diet—but AIP, Paleo, and gluten-free approaches offer powerful starting points. Each one can help reduce inflammation, support immune function, heal the gut, and restore the body’s ability to produce and respond to thyroid hormones.
By choosing foods that nourish the body and soothe the immune system, individuals with hypothyroidism and Hashimoto’s can experience profound improvements in energy, clarity, mood, and overall well-being.
True healing begins with what we choose every day—on our plate, in our thoughts, and in our hearts.
References
- Wentz, Izabella. Hashimoto’s Protocol. HarperOne.
- Kharrazian, Datis. Why Do I Still Have Thyroid Symptoms? Elephant Press.
- American Thyroid Association – https://www.thyroid.org
- National Institutes of Health – https://www.niddk.nih.gov
- Institute for Functional Medicine – https://www.ifm.org
- Fasano, Alessio. “Leaky Gut and Autoimmune Diseases” – Clinical Reviews in Allergy & Immunology, 2012.
- Vojdani A. “Immune reactivity to dietary proteins and peptides” – Journal of Clinical Immunology, 2004.
