What is The Best Autoimmune ​Diet?

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Explore what the best autoimmune diet is and discover a proven step-by-step process of how to create the best autoimmune diet for yourself in order to bring immediate relief of the debilitating unwanted symptoms caused by autoimmune conditions and inflammatory disease.

What is the Best Autoimmune ​Diet by Emily Kyle Nutrition

What is The Best Autoimmune Diet?

After writing two cookbooks focusing on the Autoimmune Paleo Protocol (AIP), surely I should have an answer to the popular question: What is the Best Autoimmune Diet?

After years of working in private practice with women just like you, who are currently living in the shadow of an autoimmune disease, my professional opinion is that there is no such thing as a single best autoimmune diet recommendation

Autoimmunity and inflammation are highly unique to each individual.

They affect each person differently mentally, physically, and emotionally as their symptoms manifest differently. No two autoimmune conditions are alike, so no two treatment plans can be alike and still be effective.

A dietary, environmental, or hormonal trigger for one person may not be the same trigger for another. This ultimately leads us to the conclusion that there is no general best autoimmune diet.

However, hope is not lost!

The best autoimmune diet is a customized anti-inflammatory, autoimmune diet that is based uniquely upon you and your own unique biochemistry.

This will allow you to create the best autoimmune diet and lifestyle for you, ultimately bringing you the quickest symptom relief and even reaching the goal of symptom remission. 

How Do You Create A Personalized Autoimmune Diet?

There are many general recommendations made for the best autoimmune diet:

However, none of these diets specifically cater to each individual, their own unique biochemistry, or their specific inflammatory triggers. 

For anyone living with Hashimoto’s or another autoimmune disease, it is widely accepted that gluten should be eliminated from the diet during an elimination phase or even indefinitely. 

It is also accepted that dairy is a pro-inflammatory food for many individuals, which is why a dairy-free, gluten-free diet is often the first step in following an elimination diet that produces results. 

But what about the rest of the foods you hear about avoiding – eggs, nightshades, nuts, legumes, and grains? Aren’t these foods that were once considered to be healthy? 

For most individuals, these are healthy ingredients that can provide an ample amount of nutrition and dietary fiber which plays a huge role in the healing of the gut microbiome by providing prebiotics.

But it is important to understand that these foods can be inflammatory to some people, especially for those who are battling an autoimmune disease.

Trying any one of these diets may bring about symptom relief, but what happens when the don’t help? What happens when one of these random diets helps a little, but not enough? What is the next step?

This leads us to Food Sensitivity Testing, the quickest, more effective way to help determine what your specific dietary triggers are so that you are not unnecessarily avoiding foods that may contribute to your overall health and well being. 

Food Sensitivity Testing Could Determine The Best Autoimmune ​Diet For You

I recommend the Mediator Release Test (MRT®) in combination with the Lifestyle, Eating and Performance Therapy (LEAP®) Protocol.

It is hands down the most strategic method of dealing with food sensitivity related illnesses that you can find anywhere in healthcare today. 

This comprehensive program was developed by a team of dietitians, physicians, immunologists, and medical business professionals with more than 100 years of combined experience in treating food sensitivity related conditions.

This test and dietary protocol have been used to successfully treat thousands of patients with IBS, migraines, rheumatoid arthritis, Hashimoto’s, fibromyalgia, ADD/ADHD, IBD, chronic fatigue syndrome, obesity, and more over the past decade. 

What is MRT Testing?

MRT is the only blood test that quantifies the inflammatory response to foods and food-chemicals, letting you know not just which foods you should stay away from, but more importantly which foods are your BEST foods – those with the lowest level of reactivity.

Independent studies confirm MRT is the most accurate and most comprehensive blood test available for food and food-chemical reactions.    

MRT is not IgG, IgA or IgE testing.

What is LEAP?

The information MRT provides directly translates into the most effective therapy – the LEAP Anti-Inflammatory Eating Plan. 

LEAP has helped thousands of patients across the country turn years of suffering into a bright, happy, healthy future, free of the symptoms that once seemed an inescapable part of life.    

Medical Conditions considered for this type of therapy include, but are not limited to:

  • Irritable bowel syndrome (IBS, IBD)
  • Rheumatoid Arthritis
  • Hashimoto’s thyroiditis
  • Acid reflux
  • Migraine and other headaches
  • Weight imbalances
  • Fibromyalgia
  • Chronic fatigue
  • Eczema skin eruptions
  • Brain fog
  • And more


The AIP Diet, also known as the Autoimmune Paleo Protocol, is a lifestyle approach to managing autoimmune and inflammatory conditions which include both dietary and holistic lifestyle modifications

The AIP Diet was designed for people diagnosed with autoimmune conditions to help identify their specific dietary triggers for inflammation, thereby reducing the immune response and manifested symptoms. 

The Autoimmune Paleo Protocol is similar to the Paleo diet but is even more restrictive during the elimination phase by removing a wide variety of potential inflammatory food triggers. 

During this phase, the diet restricts any foods that may potentially be causing inflammation in the body while simultaneously focusing on supporting and nourishing the body in an attempt to heal the gut. 

While the AIP diet cannot cure an autoimmune condition, it can help to reduce the severity of symptoms experienced and help in the overall treatment and multidisciplinary approach of treating an autoimmune disorder. 


The AIP diet focuses on consuming a wide variety of anti-inflammatory foods while removing the following food groups during the elimination phase. It is also recommended to stay away from painkillers, alcohol, and other inflammatory lifestyle behaviors during this time.


  • Dairy
  • All grains (including gluten-containing grains)
  • Eggs
  • Legumes such as beans and peanuts
  • Nightshade vegetables
  • Nuts & nut butter
  • Seeds & seed-derived spices
  • Added sugar
  • Food additives
  • Artificial sweeteners
  • Processed vegetable oils


The initial restrictive diet phase, also known as the elimination phase, is meant to allow you to feel safe consuming the foods that you are not as likely to be sensitive to while allowing your body to heal and repair itself.

After this phase, the reintroduction phase is started in order to help you accurately identify your specific triggers.

Once you are confident in identifying and understanding which foods you are sensitive to, you can feel confident in consuming the foods that you are not sensitive to. 


After writing two cookbooks on the AIP diet for thyroid conditions, I am used to hearing “so, what you can eat on the AIP diet?”

I tell my clients that while following the AIP diet, you are encouraged you to load up and enjoy meals filled with the following anti-inflammatory foods.

These are generally recognized safe foods that you are encouraged to enjoy, but it is also important to keep in mind your own personal sensitivities and allergies. 

*If possible, choose organic produce whenever possible to avoid potential chemical reactions.


  • Organic, Humanely-Raised, Pastured Meat: Chicken, turkey, duck, beef, pork, lamb, or venison
  • Wild-Caught Seafood: Salmon, cod, halibut, trout, haddock. Shellfish – shrimp, clams or mussels
  • Non-Nightshade Vegetables: All vegetables except tomatoes, bell and hot peppers, eggplant, and white potatoes
  • High-Quality Oil: Avocado oil, coconut oil, or extra-virgin olive oil
  • Healthy Fats: Avocado, coconut products, bone broth
  • Fresh or Dried Herbs: Parsley, thyme, basil, tarragon, rosemary, chives, chervil, marjoram, oregano, fennel, lavender, mint, cilantro, dill
  • Dairy-Free Fermented FoodsKombucha, kefir, and vinegar
  • Beverages: Herbal tea, homemade bone or vegetable broth

It is a combination of nutrients, antioxidants, omega-3 fatty acids, and/or plant-based dietary fiber that make these foods an excellent choice for maintaining an anti-inflammatory diet.

That does not mean these foods could not be potentially inflammatory to you and your own unique biochemistry. 


The Autoimmune Paleo Protocol (AIP) can help treat and possibly send Hashimoto’s and other autoimmune symptoms into remission―but what does that mean for your day-to-day diet?

My second cookbook, The Hashimoto’s AIP Cookbook, is the first-ever cookbook to tell you everything you need to know in order to really bring the AIP diet into your life, and I am excited to share some of my most popular recipes below.

The Hashimoto’s AIP Cookbook helps heal immune conditions with deliciously nutritious and simple recipes. With options for 30-Minute, 5-Ingredient, One-Pot, and Make-Ahead meals, these recipes make this diet surprisingly easy.

AIP Diet Recipes

Looking for more recipes? Check out these Autoimmune Paleo Protocol recipes featured on my blog.

AIP Drink Recipes

AIP Breakfast Recipes

AIP Sauces & Side Dishes

AIP Entrees

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