The Worst Foods to Eat With Autoimmune Disease

by JJ Virgin on May 16, 2023

Autoimmune diseases like celiac disease, multiple sclerosis, Hashimoto’s thyroiditis, and type 1 diabetes occur when your immune system goes haywire and mistakenly attacks healthy tissues.  

Scientists have identified at least 80 autoimmune diseases, and four out of five people diagnosed are women.1 (Researchers speculate that sex hormones and environmental factors could be clues as to why they occur more often in women.2

Chronic inflammation plays a big role in most autoimmune conditions.3 Among its damage, this simmering, low-grade inflammation makes your immune system more likely to mistake healthy cells for foreign invaders and attack them. 

Chronic inflammation can contribute to a syndrome called leaky gut, where your intestinal wall becomes more permeable. Those gaps allow harmful substances to enter the bloodstream. The immune system then overreacts, producing antibodies to destroy these food particles. Unfortunately, those antibodies can react with healthy tissues, leading to autoimmune reactions.4 

The Worst Foods to Eat With Autoimmune Disease 

The foods you eat underlie chronic inflammation, leaky gut, and other problems. When you have an autoimmune disease, the right foods can cool down inflammation and reduce the symptoms that accompany your condition.  

And the wrong foods? They can trigger or exacerbate symptoms. When it comes to the worst foods to eat with autoimmune disease, these five are the biggest troublemakers. 

1. Gluten 

When it comes to managing autoimmune disease, gluten has to go. Weight gain, digestive upset, headaches, joint pain, anxiety, depression, and especially leaky gut are frequent signs that you’re intolerant to gluten.  

But with autoimmune disease, the damage can get even worse.  

One of the most common autoimmune conditions is Hashimoto’s thyroiditis, in which your immune system doesn’t recognize your thyroid and attacks it. This disease is four to 10 times more common among women than men.5 

Here’s how gluten makes it worse: The primary protein in gluten, called gliadin, looks like thyroid tissue. When you have leaky gut and eat gluten, gliadin can slip through the gut wall and trigger an immune response that can last up to six months.6 

Regardless of whether you have Hashimoto’s or another autoimmune disease, you’re probably sensitive to gluten.7 I’ve found that 90% of people who pull it out feel better, and I’m convinced the other 10% didn’t remove it completely. 

2. Dairy 

The whole Got Milk? campaign misled an entire generation to believe we need milk to be healthy. Nothing could be further from the truth

Dairy contains two proteins, casein and whey, which can be a problem for people with autoimmune diseases. Some people have a primary sensitivity to dairy, meaning their body reacts when they consume it. For others, a secondary sensitivity to dairy proteins results from gluten-induced damage to the gut.8 

Regardless of your degree of sensitivity, dairy is bad news for autoimmune disease. Researchers have looked at how dairy products like milk, cheese, and yogurt can worsen inflammation in autoimmune diseases, often focusing on specific conditions. In one study, researchers found that cow’s milk can trigger an autoimmune response for people with type 1 diabetes.9 

Other studies show that some people with multiple sclerosis may have an autoimmune response to cow’s milk. Cross-reactions to dairy mean that your body mistakenly attacks and destroys myelin, the fatty substance that covers and protects the fibers in your brain and nervous system. With that myelin damage, the signal transmission is disrupted between your brain and the rest of the body.10 

3. Soy 

There’s no joy in soy, especially when you have an autoimmune disease. According to Izabella Wentz, PharmD, about 41% of people with Hashimoto’s are sensitive to soy and 60% of them report gut symptoms (such as abdominal pain) when they eat soy.11 

Among its problems, soy is relatively high in anti-nutrients called lectins. These proteins can bind to the lining of the gut and interfere with nutrient absorption. Their “stickiness” makes lectins resistant to digestion, allowing them to enter your bloodstream unchanged.  

Lectins can also damage the intestinal lining, leading to increased intestinal permeability and leaky gut. This allows undigested food particles and other toxins to enter the bloodstream, which can trigger or exacerbate an immune response. 

Once absorbed, lectins can bind to many tissues, including the thyroid, pancreas, and collagen in your joints. They then attract white blood cells to these tissues, potentially leading to an autoimmune response.12  

4. Sugar (In All Its Many Forms) 

Whether you have an autoimmune disease or not, sugar is off the table. People who consume large amounts of sugar and other carbohydrates have an increased risk of developing an autoimmune disease.13 High levels of sugar also stimulate the production of inflammatory cytokines, which activate your immune cells and increase the risk of autoimmune reactions.14  

For those with autoimmune disease, sugar can ramp up chronic inflammation, creating more tissue damage and worsening their condition.15 

Sugar can also contribute to the gut havoc that creates or exacerbates autoimmune conditions. Excess sugar disrupts the trillions of gut bacteria, for one, leading to an imbalance called dysbiosis.16 Studies show that dysbiosis can drive autoimmune diseases, including type 1 diabetes, rheumatic arthritis, and multiple sclerosis.17 

5. Nightshade Vegetables 

If you’ve read The Virgin Diet, you’re familiar with how soy, gluten, dairy, and added sugar can create problems in your gut and beyond. Finding nightshade vegetables on this list, however, may surprise you.  

Aren’t vegetables healthy? Normally, yes, but a few of them like tomatoes, eggplants, peppers, and potatoes—collectively called nightshade vegetables—can trigger inflammation in individuals with autoimmune diseases.  

Naturally produced compounds in nightshade vegetables, called glycoalkaloids, can:  

  • Increase chronic inflammation 
  • Put your immune system in overdrive 
  • Contribute to leaky gut 

All of these factors cumulatively contribute to autoimmune disease.18 People with autoimmune diseases often find that avoiding nightshade vegetables reduces symptoms, including joint pain and inflammation. 

Managing Autoimmune Disease Starts With Your Gut  

You may be surprised how much you can heal if you make food your medicine. While many autoimmune diseases result from a combination of genetic, environmental, and other factors, diet definitely plays a role in developing or worsening them. Eating the wrong foods repeatedly can trigger or exacerbate autoimmune diseases. 

In her book Hashimoto’s Food Pharmacology, Wentz talks about a survey of over 2,000 folks with Hashimoto’s. Among her findings:  

  • 81% of people felt better following a grain-free diet 
  • 79% of people felt better off dairy 
  • 63% felt better off soy 
  • 76% of people felt better eating a diet that balanced their blood sugar levels19 

I’ve personally seen how breaking free of food intolerance can improve inflammation, gut conditions including leaky gut, and autoimmune conditions. I also know how hard it can be to give up these foods, which are often sneaky and “hide” under different names. 

From that approach, I created the 21-Day Breakthrough Food Intolerance Cleanse. This self-paced online program has all the tools and resources you need to help calm inflammation from hidden food sensitivities, lose fat, reclaim your health, and feel energized and better than ever.* 

The program includes: 

  • 12 in-depth video lessons walking you through the protocol, plus daily tips and resources to boost your success 
  • Weekly meal plans and shopping lists (omnivore and plant-based) 
  • Body-measurement and symptoms trackers to monitor your progress and success throughout the program 
  • Guides for dining out and making healthy food swaps so you can take your healthy habits on the go 
  • Access to our exclusive Facebook group for motivation, support, and guidance from JJ’s team of coaches 
  • Exclusive discounts on your purchases in the JJ Virgin store 

Learn more about and purchase the 21-Day Breakthrough Food Intolerance Cleanse here. 


  1. Angum F, Khan T, Kaler J, Siddiqui L, Hussain A. The Prevalence of Autoimmune Disorders in Women: A Narrative Review. Cureus. 2020 May 13;12(5):e8094. doi: 10.7759/cureus.8094. PMID: 32542149; PMCID: PMC7292717. 
  2. Kronzer VL, Bridges SL Jr, Davis JM 3rd. Why women have more autoimmune diseases than men: An evolutionary perspective. Evol Appl. 2020 Dec 1;14(3):629-633. doi: 10.1111/eva.13167. PMID: 33767739; PMCID: PMC7980266. 
  3. Duan L, Rao X, Sigdel KR. Regulation of Inflammation in Autoimmune Disease. J Immunol Res. 2019 Feb 28;2019:7403796. doi: 10.1155/2019/7403796. PMID: 30944837; PMCID: PMC6421792. 
  4. Bioscience Horizons: Intestinal permeability and autoimmune diseases 
  5. National Institute of Diabetes and Digestive and Kidney Diseases: Hashimoto’s Disease  
  6. Pedre, Vincent. Happy Gut (pp. 53-54). HarperCollins. Kindle Edition. 
  7. PharmD, Izabella Wentz . Hashimoto’s Food Pharmacology (p. 59). HarperCollins. Kindle Edition. 
  8. PharmD, Izabella Wentz . Hashimoto’s Food Pharmacology (p. 60). HarperCollins. Kindle Edition. 
  9. Monetini L, Cavallo MG, Manfrini S, Stefanini L, Picarelli A, Di Tola M, Petrone A, Bianchi M, La Presa M, Di Giulio C, Baroni MG, Thorpe R, Walker BK, Pozzilli P; IMDIAB Group. Antibodies to bovine beta-casein in diabetes and other autoimmune diseases. Horm Metab Res. 2002 Aug;34(8):455-9. doi: 10.1055/s-2002-33595. PMID: 12198602. 
  10. Chunder R, Weier A, Mäurer H, Luber N, Enders M, Luber G, Heider T, Spitzer A, Tacke S, Becker-Gotot J, Kurts C, Iyer R, Ho PP, Robinson WH, Lanz TV, Kuerten S. Antibody cross-reactivity between casein and myelin-associated glycoprotein results in central nervous system demyelination. Proc Natl Acad Sci U S A. 2022 Mar 8;119(10):e2117034119. doi: 10.1073/pnas.2117034119. Epub 2022 Mar 2. PMID: 35235454; PMCID: PMC8916005. 
  11. Thyroid Pharmacist: How Avoiding Soy Can Benefit Hashimoto’s  
  12. Vojdani A, Afar D, Vojdani E. Reaction of Lectin-Specific Antibody with Human Tissue: Possible Contributions to Autoimmunity. J Immunol Res. 2020 Feb 11;2020:1438957. doi: 10.1155/2020/1438957. PMID: 32104714; PMCID: PMC7036108. 
  13. Immunopaedia: Sugar and autoimmune diseases: what are the risks? 
  14. Science Daily: How sugar promotes inflammation 
  15. Ma X, Nan F, Liang H, Shu P, Fan X, Song X, Hou Y, Zhang D. Excessive intake of sugar: An accomplice of inflammation. Front Immunol. 2022 Aug 31;13:988481. doi: 10.3389/fimmu.2022.988481. PMID: 36119103; PMCID: PMC9471313. 
  16. Satokari R. High Intake of Sugar and the Balance between Pro- and Anti-Inflammatory Gut Bacteria. Nutrients. 2020 May 8;12(5):1348. doi: 10.3390/nu12051348. PMID: 32397233; PMCID: PMC7284805. 
  17. Mousa WK, Chehadeh F, Husband S. Microbial dysbiosis in the gut drives systemic autoimmune diseases. Front Immunol. 2022 Oct 20;13:906258. doi: 10.3389/fimmu.2022.906258. PMID: 36341463; PMCID: PMC9632986. 
  18. Rheumatoid Arthritis Foundation: Should I eat Nightshade Vegetables? 
  19. PharmD, Izabella Wentz . Hashimoto’s Food Pharmacology (p. 28). HarperCollins. Kindle Edition. 

*These statements have not been evaluated by the Food & Drug Administration. Products mentioned are not intended to diagnose, treat, cure, or prevent any disease. The views in this blog by JJ Virgin should never be used as a substitute for professional medical advice. Please work with a healthcare practitioner concerning any medical problem or concern.