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Switching to a Dairy-Free Diet for Hashimotoʼs 

How & why to eliminate dairy if it triggers your Hashimoto's symptoms. 
Switching to a Dairy-Free Diet for Hashimotoʼs 
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In this article:

  • What is problematic about dairy?
  • What is an allergy vs. sensitivity?
  • How to use an elimination diet like the autoimmune protocol (AIP)
  • AIP-compliant dairy alternatives

Dairy products are a controversial food source. From one perspective, dairy can be excellent sources of calcium, vitamin D, potassium, and some vitamins - especially in their raw and fermented states! In a single glass of milk, most people can get almost every nutrient their body needs. 

However, from an evolutionary standpoint, our human ancestors did not eat or drink milk products, especially from other animals. There are some arguments that our bodies are still incapable of digesting milk in adulthood.

Most forms of dairy we eat today are highly processed with added preservatives and hormones. These additives can wreak havoc on our digestive system and can trigger inflammation. 

Of course, not all inflammation is harmful. Inflammation is a vital part of the immune system's response to healing injuries and infections. But the type of inflammation that is problematic is chronic low-grade inflammation, often caused by dietary and lifestyle factors.

Chronic inflammation may reduce total thyroid receptor count and can disrupt thyroid hormone function. Additionally, if you have lactose intolerance, you may suffer from malabsorption of essential nutrients and oral medications - including your thyroid hormone replacement medication.

There's a high correlation between autoimmune symptoms and food sensitivities. More specifically, people with Hashimoto's disease tend to be more sensitive to specific proteins found in dairy products. They also tend to have a higher incidence of lactose intolerance. 

What is problematic about dairy?

Dairy products contain certain nutrients that are difficult for the human gut to digest. Lactose is the primary carbohydrate (or sugar) in milk and provides direct energy to your body. The enzyme lactase breaks lactose into two simple sugars, glucose and galactose. 

At birth, our digestive system has plenty of the lactase enzyme to digest lactose in human breastmilk. The effectiveness of lactase declines in most populations once we wean from breastmilk. People from some regions of the world, such as northern Europe, are less likely to suffer from a decline in lactase activity. This predisposition is because milk products were an essential part of their ancestor's diets. Studies find that genes have been modified throughout generations to improve the expression of lactase and overall digestion of milk products.

Most of the world's population struggles to digest lactose. While lactose intolerance is not necessarily harmful to your health, it can lead to uncomfortable symptoms such as bloating, gas, and diarrhea. Some people also find that lactose contributes to psychological symptoms such as stress and mood swings. 

Casein and whey are two other ingredients in milk products that can contribute to digestive troubles. Both casein and whey are the two milk proteins that contain all the essential amino acids. Generally, casein and whey are easy to digest. However, people can have a true food allergy to casein and whey. Indeed, when a person has a milk allergy, they are allergic to the protein in milk. Some people have mild allergic reactions to milk proteins (such as eczema and bloating), whereas others can develop an anaphylactic reaction.


What is an allergy vs. sensitivity?

Food allergies and sensitivities are terms that people often use interchangeably to describe unpleasant symptoms caused by eating certain foods. However, there is an important distinction between allergies and sensitivities that is critical and sometimes life-threatening.   

An allergy is when your immune system reacts to a specific protein found in food. When the protein is recognized, the immune system rapidly creates antibodies to fight the protein and protect your body. 

There are different branches of your immune system. When you have an allergy, the IgE (immunoglobulin-E) branch of your immune system is activated, which causes your immune cells to release histamine.

Symptoms of an allergic reaction include:

  • Hives
  • Swelling
  • Difficulty breathing
  • Stomach upset (vomiting and diarrhea)
  • Dizziness
  • Wheezing
  • Death


Unlike an allergy that stems from the immune system, food sensitivity is a reaction from your digestive system. Food sensitivity is much more common than a food allergy. Sensitivity stems from your gut's inability to digest or absorb a specific food or group of foods. Often, sensitivity refers to an intolerance, such as in lactose intolerance. 

A food sensitivity is not life-threatening. However, a person usually discovers they are sensitive to a specific food or food group when they develop unpleasant digestive symptoms.

Symptoms of food sensitivity include:

  • Nausea
  • Abdominal cramping and bloating
  • Gas
  • Diarrhea
  • Constipation

People often have a sensitivity because they do not have the right digestive enzymes, are sensitive to additives or preservatives, or cannot tolerate certain chemicals such as caffeine. 

How to use an elimination diet like AIP

An elimination diet is the best place to start if you find that your Hashimoto's symptoms might be related to the foods that you eat. One of the leading diets for people with autoimmune disorders is the autoimmune protocol (AIP) diet.

The AIP diet is a protocol designed to reduce inflammation for those with autoimmune conditions. The diet consists of a strict elimination phase followed by a slow and intentional reintroduction phase. This process allows your gut and microbiota to resettle and reset before you reintroduce foods to figure out which individual foods contribute to adverse autoimmune responses. 

During the elimination phase, you start by removing grains, gluten, dairy, soy, sugar, eggs, and nuts and seeds for several weeks. Many people will also eliminate other possible dietary triggers like nightshades (potatoes and tomatoes), caffeine, alcohol, and legumes. 

You may see improvement in your symptoms during the elimination phase. There aren't any hard and firm rules on when to reintroduce foods on the AIP diet, though ideally, you wait to reintroduce foods until you feel terrific and symptom-free. Don't be in a hurry to reintroduce foods! The longer you wait between each food, the more likely you are to be successful in discovering your triggers.

If you have a recurrence of symptoms once you reintroduce dairy, it is safe to assume that this food group is a trigger of your symptoms. 

AIP compliant dairy alternatives

Cow's milk alternatives

Coconut milk is the best non-dairy milk alternative. It is AIP-friendly. Oat, hemp seed, almond, flaxseed, and cashew milks are not AIP-compliant because they come from nuts and seeds. Still, they are a better option than cow's milk to heal your gut and reduce symptoms. 

Butter alternatives

Try using coconut oil or coconut butter (also called coconut manna). Lard is also an AIP-friendly alternative for butter.

Yogurt alternatives

Again, coconut yogurt is the best non-dairy yogurt alternative. It is AIP-friendly. Almond milk, oat milk, and soymilk yogurts are not AIP-compliant. Coconut yogurt is available in some stores but sometimes includes non-AIP compliant ingredients like added sugar. Be sure to carefully read nutritional labels or try an at-home coconut yogurt recipe. (You can also make delicious ice cream from coconut milk!)

Cheese alternatives

Nutritional yeast has been used for a long time in vegan diets and is AIP-compliant. If you purchase a store-bought "cheese" product made from nutritional yeast, verify the label does not contain any additives that would compromise the AIP protocol.

BONUS: try coconut-milk kefir!

Coconut water kefir or coconut milk kefir is very beneficial for digestion and gut health. We like it because it's high in nutrients and probiotics too!

A note from Paloma Health

Many nutritional factors play a role in optimizing thyroid function. Paloma Health offers you the opportunity to work with a nutritionist in collaboration with a physician to determine nutritional status for optimal thyroid health.

Join us in the Thyroid Care Club Facebook Group for more on these topics and many others regarding thyroid health and well-being.


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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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