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Why Are Fermented Foods Good for Hypothyroidism?

Learn why fermented foods are not only good for the immune system but also for thyroid function.
Why Are Fermented Foods Good for Hypothyroidism?
Last updated:
2/16/2025
Written by:
Medically Reviewed by:

The Big Picture

A healthy gut plays a crucial role in supporting your immune function and thyroid health, particularly if you have Hashimoto’s thyroiditis, an autoimmune thyroid condition commonly linked to celiac disease and non-celiac wheat sensitivity. A compromised gut barrier can lead to increased intestinal permeability, or "leaky gut," allowing harmful antigens to trigger immune reactions and potentially cross-react with thyroid tissue. Additionally, a well-functioning gut is essential for absorbing critical micronutrients such as iodine, iron, copper, selenium, zinc, and vitamin D—nutrients that are vital for thyroid hormone production, conversion, and immune regulation. Fermented foods, rich in probiotics, can help restore your gut balance and support digestion, positively impacting thyroid function. These include kefir, sauerkraut, kimchi, yogurt, and kombucha, among others. The fermentation process enhances nutrient availability, reduces non-nutrients, and introduces beneficial microbes that may offer anti-inflammatory, antioxidant, and antimicrobial effects.

While probiotics in supplement form may benefit those with specific gastrointestinal conditions, some people can obtain sufficient beneficial bacteria from a diet rich in fermented foods. However, you should be mindful when selecting store-bought fermented foods, as some are pasteurized or loaded with additives that diminish probiotic benefits. For those interested, homemade fermentation is a simple and cost-effective way to incorporate probiotics, requiring only fresh vegetables, clean glass jars, and a natural fermentation starter such as salt or a bacterial culture. Ultimately, working with a thyroid nutritionist can help you tailor a diet that optimally supports your gut and thyroid health.

Listen to this article at "My Thyroid Health," the Paloma podcast

A healthy gut is not only good for the immune system but also for thyroid function. In fact, Hashimoto's thyroiditis (an autoimmune attack of the thyroid gland) commonly occurs with Celiac disease and non-Celiac wheat sensitivity. 

A damaged gut barrier may cause increased intestinal permeability (commonly known as leaky gut), allowing antigens to pass through and trigger the immune system or cross-react with tissues outside the intestines.

Additionally, the health of your gut influences the availability of essential micronutrients for the thyroid gland. Iodine, iron, and copper are crucial for creating thyroid hormone, selenium and zinc help with thyroid hormone conversion, and vitamin D helps regulate the immune response. People with Hashimoto's thyroiditis are often deficient in these micronutrients, resulting in frustrating thyroid-related symptoms. 

Eating probiotics found in fermented foods supports digestion and shows positive effects on thyroid function. 

What are fermented foods?

Fermentation is an age-old technique still used today to preserve food. The fermentation process breaks down carbohydrates like starch and sugar using bacteria and yeast to make food come (literally) alive with good bacteria. 

Common fermented foods include: ‍

  • Kefir
  • Sauerkraut
  • Tempeh
  • Kombucha
  • Kimchi
  • Yogurt
  • Sourdough bread
  • Beer and wine

During the transformative fermentation process, the added bacteria prepare vitamins and minerals to be used by the body, remove some non-nutrients, and produce beneficial microbes. Research suggests that fermented foods offer a range of health benefits as a result. Benefits may include anti-oxidant, anti-microbial, anti-fungal, and anti-inflammatory effects. 

Healthy gut, healthy thyroid

Hypothyroidism, or an underactive thyroid, manifests in the body as decreased metabolic functions. Hypothyroidism affects virtually every system in your body, including your gastrointestinal tract (a.k.a, your gut).

Generally speaking, the thyroid is sensitive to changes in the gut microbiome. A well-balanced gut supports metabolic functions like digestion, nutrient absorption, detoxification, and vitamins' synthesis. Beneficial bacteria maintain your gut barrier integrity and help maintain an acidic environment to discourage pathogenic bacteria from moving in.

Often, people with Hashimoto's thyroiditis, an autoimmune thyroid condition, have an imbalanced gut microbiome—meaning that there are more bad bacteria than good bacteria in the gut's environment. There is evidence that the gut microbiome and thyroid autoimmunity influence one another, and an imbalance can lead to leaky gut.

An imbalance may lead to a leaky gut which means that your intestinal junctions' integrity is weak, allowing microorganisms to escape into your bloodstream. In some cases, when this happens, your immune system attacks them, thinking they are foreign invaders. 

Fermentation produces beneficial microbes (a.k.a probiotics) that can introduce helpful bacteria to pathogenic bacteria's overgrowth. Rebalancing the bacteria in the gut through these fermented foods, probiotic supplements, or medication can help support gut health.

Generally speaking, probiotics are helpful in the treatment and prevention of gastrointestinal issues. In the form of supplements, probiotics are likely not necessary for most individuals. Research really only supports their use in individuals with IBS or related diagnosed conditions.

Safety precautions and side effects

Fermented foods are considered safe for most people. However, studies show that some people may experience minor digestive symptoms like cramping, nausea, irregular stools, and gas. These side effects are only temporary due to the high probiotic content of fermented foods that cause colonic activity.

Look for fermented foods that are refrigerated, not room-temperature jars or cans. Refrigeration ensures that active cultures stay alive. 

Pay attention to nutrition labels to choose the healthiest option for you. Some pickled foods are mass-produced and treated with sodium, citric acid, or other chemicals that do not allow probiotics to develop appropriately. You want to see mention of live bacteria, fermented, or probiotics on the label, not high levels of sugar, salt, or fat. Only pure fermentation, without pasteurization (sterilization through heat), produces probiotic enzymes and all their benefits. 

You can also ferment foods at home. Be sure to keep correct temperatures, fermentation times, and sterile equipment to avoid spoiled, unsafe food.

How to ferment food at home

Fermenting at home is relatively cheap and easy. (Plus, you'll impress all your friends!) Lacto-fermentation is one of the most common fermentation processes. Lacto refers to the Lactobacillus bacteria, which transforms sugars into lactic acid during ferment.

Pick your produce

Organic produce is preferred because the good bacteria stay intact due to it not being sprayed with pesticides. Hearty vegetables like cabbage, carrots, cauliflower, or celery also better maintain their crunch after fermentation. 

Find a container

No need to get fancy. Any glass jars will do! Make sure to clean them thoroughly with soap and water and let them dry. You don't want any harmful bacteria hanging out in there. 

Decide to use salt or a fermentation starter

The method you choose may depend on personal taste or special dietary requirements. A fermentation starter is a microbiological culture that contains bacterial strains that perform fermentation. Find a friend who is willing to give you some of theirs, or buy a powdered starter online. If using salt, try Himilayan, kosher, pickling, or sea salt. Avoid iodized salt as it may inhibit the culturing process.

Mix and wait

Put your veggies, seasoning, and starter in your jars, and then cover with filtered water. Put your jars in a cool, dark place, and wait for one to two weeks until you see probiotic activity. Remember: bubbles are a sign of life! 

Move vegetables to cold storage

Once your veggies are fermented, move them into the fridge, where they will store for several months to enjoy! 

A note from Paloma Health

We recommend that you work with a thyroid nutritionist to develop a way of eating that works for you individually. Our registered dietitian nutritionists can help you identify dietary triggers and reverse nutritional deficiencies.

Key points

  • Gut health plays a crucial role in immune function and thyroid health, with conditions like Hashimoto’s thyroiditis often linked to celiac disease and non-celiac wheat sensitivity.
  • A damaged gut barrier can lead to leaky gut, allowing harmful antigens to trigger immune responses and potentially impact thyroid function.
  • Essential micronutrients for thyroid health, such as iodine, iron, selenium, and zinc, depend on proper gut function for absorption, and deficiencies are common in Hashimoto’s patients.
  • Fermented foods like kefir, sauerkraut, kimchi, and yogurt contain probiotics that support gut balance, aid digestion, and may help regulate immune responses affecting thyroid function.
  • An imbalanced gut microbiome, common in Hashimoto’s, can lead to inflammation and leaky gut, but probiotics from fermented foods or supplements can help restore microbial balance.
  • When choosing fermented foods, opt for refrigerated, non-pasteurized options with live probiotics, or consider fermenting at home using organic produce and proper fermentation techniques.

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Katie Wilkinson

Katie Wilkinson, previously serving as the Head of Content and Community at Paloma Health, fervently explores the nexus between healthcare and technology. Living with an autoimmune condition, she's experienced firsthand the limitations of conventional healthcare. This fuels both her personal and professional commitment to enhancing patient accessibility to superior care.

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