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Hashimoto's Prescription Diet: Food and Supplement Protocol Strategy (Part III)

I'm an accredited journalist working at the intersections of science, food and public health. I am also a certified nutritionist.

A helpful look into the Hashimoto diet

A helpful look into the Hashimoto diet

Part II laid out the rationale for building a holistic nutrition protocol that supports the thyroid and immune system. This third article provides its exact steps, some dos and don'ts and supplement recommendations.

Managing Hashimoto's with Diet

Below are the steps you can take in order to potentially improve your Hashimoto's with certain eating habits.

Step 1: Remove Autoimmune Triggers

An essential step to better manage the condition is cutting out all possible triggers mediating autoimmune flare-ups by affecting neuroendocrine hormones (stress), the gut (gluten and gluten-like food) or detoxification (environmental toxins).

Gluten cross-reactive foods include instant coffee; cow's milk; whey protein; oats; yeast; millet; corn; rice; sesame; buckwheat; sorghum; hemp; amaranth; quinoa; tapioca; teff; potato; soy and egg.

Some people with Hashimoto's give up gluten and feel only marginally better. In this case, the paleo Autoimmune Protocol (AIP) is a helpful nutritional framework.

The AIP is a diet free of grains, starchy vegetables, legumes, and most sweeteners. It is void of all dairy, eggs, corn, soy, yeast, nuts, and every other food allergen known to man.

Because the AIP is a stricter diet plant, it may not be sustainable for many people over the long term. Still, it can be used as an elimination diet to identify one's sensitivities before transitioning to a healthy maintenance diet.

A balanced iodine intake is also recommended, as this nutrient can worsen the autoimmune attack on the thyroid, especially in those with a selenium deficiency.

Step 2: Enhance Immunity

Hashimoto's patients will want to favour a nutritionally-dense diet, with foods rich in nutrients that promote a healthy human system, such as vitamin C, vitamin D, zinc, selenium and iron.

The other facet of a diet supporting optimal immune function is consuming foods that feed the correct type of gut microbes. A strong and diverse microbiome is closely tied to the integrity of the gut barrier, preventing leaky gut and stimulating proper immune cell activity.

First, we want to ensure we are ingesting enough prebiotic foods (like garlic, onions, leeks, asparagus, Jerusalem artichokes, and dandelion greens) and probiotic foods - including kefir, fermented vegetables, sauerkraut, tempeh, kimchi or miso.

These dietary changes promote optimal regulatory T Cell function to turn off the immune attacks against the thyroid. Patients can also supplement specific strains of probiotics to influence the Th1 and Th2 balance in the cellular immune response. Ideally, Th1 and Th2 cells are balanced, but one of the two (often the Th1 response) is on overdrive with autoimmune disease.

Try the AIP diet to remove autoimmune triggers.

Try the AIP diet to remove autoimmune triggers.

Step 3: Reduce Inflammation

Essential Fatty Acids like EPA and DHA are critical fats to control inflammation and keep the brain functioning well.

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A major benefit of increasing the intake of omega-3 fatty acids is that they have been shown to help balance the Th1 and Th2 systems.

In one person, Hashimoto could present as a Th1-dominant condition. In another, it may show as Th2 dominant. In still another, both the Th1 and Th2 systems might be overactive or underactive. So supplementing with EFAs may be one way to establish equilibrium.

EFAs also help lower the count of bacterial endotoxins called lipopolysaccharide (LPS) that notoriously contribute to a leaky gut and create excessive inflammation in the body from the GI tract.

When increasing EFAs, it's important to keep an ideal ratio of omega 3 to omega 6 by choosing to source them via fatty fish rather than seed oils, for example.

Step 4: The Extra Mile (Further Steps by Food Type)

Water and Beverages

Due to the links between Hashimoto's and low stomach acid, it is a good idea to increase the amount of water one drinks between meals and avoid drinking 20 minutes before or after meals to avoid diluting gastric juices.

For example, hot lemon water first thing in the morning helps kick-start stomach acid production to digest subsequent meals.

Salt is also important for those with hypothyroidism because it can help raise body temperature, help cells respond to thyroid hormones, and increase intestinal motility. I recommend using Celtic sea salt or a quality electrolyte powder diluted in the drinking water.

Whole Grains, Fruit and Vegetables

People with hypothyroidism have chronic digestive issues and should aim for 30–40 grams of fibre daily. However, sourcing fibre from the right foods is paramount.

People with Hashimoto's will want to plan their meals around non-starchy vegetables (as opposed to root vegetables) like green leafy vegetables to add fibre, vitamins and minerals to the diet.

Starchy vegetables (like potatoes) contain too many simple sugars that convert to glucose rapidly. As explained earlier, keeping blood sugar within the normal range has positive ripple effects on the chronic management of Hashimoto's.

Whole grains, fruits and vegetables are vital.

Whole grains, fruits and vegetables are vital.

Fats, Dairy and Refined Foods

Fats should be a significant component of all meals because they help create more energy and balance the endocrine system.

Fat is needed to make the necessary hormones, but if the body is not getting enough of the right kind of fat, it will also lead to hormone imbalances.

Vegetable oil-containing foods, like margarine, should be phased out of the diet entirely for their high levels of polyunsaturated, omega-6 fats. These foods also comprise all those made with modified fats, including palm oil, kernel oil, soybean oil, canola and sunflower oil.

Vegetable oils are highly inflammatory, and their polyunsaturated fats affect the cell structure, causing miscommunication and disrupting hormonal balance. Instead, one should switch to olive oil, raw organic butter, or ghee.

Plant: Animal Protein Ratio

Staying mindful of the ratio of animal protein (meat, fish) eaten versus plant protein, such as seeds, will help meet fibre requirements to keep a healthy microbiome.

Secondly, meats contain a high amount of the amino acid tryptophan, which can suppress the thyroid when consumed in large quantities.

Opting for easily assimilated animal protein, such as beef and chicken bone broth, is also beneficial. These contain the amino acids L-proline and L-glycine, which can help repair the digestive lining and improve hypothyroidism.


Selenium is part of several powerful antioxidant systems that dampen excessive immune responses and fight inflammation by producing selenoproteins such as glutathione peroxidase. By extension, it affects antibody production. Selenium is also required to produce thyroid hormone and convert T4 to T3.

Making sure that selenium intake is sufficient in the diet or supplements should be a consideration in a well-rounded Hashimoto nutrition plan. Part IV of this article series provides recommendations to meet that goal.

Eating fish like salmon is a great way to decrease your risk of inflammation.

Eating fish like salmon is a great way to decrease your risk of inflammation.

Hashimoto's Diet Dos

Living with an autoimmune disease comes with a responsibility to become nutritionally street smart and skilled at scouring labels for potential food allergens. Cleaning up the diet of all autoimmune triggers mentioned in step 1 of the earlier section will go a long way towards building a solid nutrition framework.

Maintaining a good omega 3 to omega 6 balance by regularly eating healthy fish like wild-caught Alaskan salmon is a great way to keep inflammation in check.
Choosing the highest quality sources of animal-based omega 3s is recommended to ward against heavy metals or other types of contamination.

In light of the above caveats regarding animal proteins, being mindful of portion control is an advantage. It is good practice to avoid having any macronutrient portion - the size of the carbohydrate, fat, or protein serving on the plate - exceed something one can hold in their hand. Smaller portions also make it easier for the body to digest the meal.

Hashimoto's Diet Don'ts

At the risk of sounding like a broken record, one should avoid gluten-containing grains AND grains that cross-react with gluten. This includes any "green-washed" multi-cereal type loaves of bread susceptible to containing rye or hybrids of wheat like spelt and kamut.

Reducing the allergenic load further means abstaining from dairy, nightshades and alcohol. It is also good to eliminate sugars in all their forms as they often cause a sympathetic nervous system reaction.

Some thyroid experts have expressed concern about thyroid disease patients going a step further and trying a low-carb diet.

However, from my research, I believe it to be a non-issue - when consuming an adequate amount of calories - to normalise thyroid function without consuming added carbs. But always check with your doctor or dietitian.

Regardless of whether or not the diet is low-carb, harmful foods to avoid at all costs include:

  • All vegetable margarine and oils
  • Commercial bread (even gluten-free) formulated with bromides (iodine antagonists), chlorine and fluorides
  • Simple sugars, including coconut sugar (because of high levels of fructose)
  • All grains, so-called ancient grains and pseudo-grains
  • All dairy
Supplements can help. Here are some suggestions.

Supplements can help. Here are some suggestions.

Must-Have Dietary Supplements

Vitamin D3 (with plenty of healthful fats)

D3 helps to regulate the immune system by influencing regulatory T cells and balancing the Th1/Th2 response.

Thorne Research D3 (1,000iu) – 5,000 IU total/daily in winter, 2,000 IU in summer, or 2 to 5 capsules daily. Or Solgar 4000IU Vitamin D3 – 1 capsule daily.

Collagen Hydrolysate

The amino acids glycine and proline are crucial for optimal immune function. Gelatin also improves digestion by binding with water to help move food through the digestive tract.

Great Lakes Gelatin or Wellgard Bovine Collagen Peptides Powder or Pure Health Collagen Protein Powder - 1 scoop (12g) daily in smoothies, hot drinks or baked goods.

Methylated B Vitamins

A vitamin-B complex (thiamine, in particular) will help with digestive complaints, general tiredness and reducing antibodies.

Swanson's Activated B Complex or Pure Encapsulations B-Complex Plus – 1 capsule daily with breakfast.


Thyroiditis attacks classically happen in the middle of the night. Magnesium is a mineral in which most people with hypothyroidism are deficient and can benefit from supplementing to promote more restful sleep.

Thorne Research Magnesium Citramate (contains a blend of magnesium citrate and magnesium malt, which helps increase absorption when combined) - 1 capsule before bed to help with nighttime thyroiditis symptoms.

Pure Encapsulations Magnesium (Glycinate), if dealing with insomnia - 3 capsules 30 minutes before bed.

Omega-3 Fish Oil

Omega 3s help balance the Th1/Th2 response, help cells communicate, reduce inflammation, and produce necessary hormones.

Nordic Naturals Ultimate Omega range – 4 capsules/daily or Carlson Maximum Omega 2000.

Optional: Gelatinized Maca Root

Maca is an adrenal adaptogen to regulate hormones and manage stress while enhancing drive. Other adaptogenic herbs can be substituted but will have variable effects depending on symptoms. It is always best to check with a dietitian or herbalist to develop the best supplement protocol. However, Maca is relatively harmless.

Gaia Herbs Maca Root – 3 caps daily (1,500 mg) away from meals.

Keep Reading

The final part IV delivers a sample 7-day menu with recipes tailored to Hashimoto's patients.

Sources and Further Reading

This content is for informational purposes only and does not substitute for formal and individualized diagnosis, prognosis, treatment, prescription, and/or dietary advice from a licensed medical professional. Do not stop or alter your current course of treatment. If pregnant or nursing, consult with a qualified provider on an individual basis. Seek immediate help if you are experiencing a medical emergency.

© 2022 Camille Bienvenu

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