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The Best Food Alternatives Guide for Autoimmunity

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The foods we eat will impact autoimmunity. However, that doesn’t mean foods can’t still be delicious and enjoyable. Luckily, there are so many healthy, autoimmune-friendly food alternatives to common inflammatory ingredients.

Autoimmune trigger foods like flour, butter, and chocolate

Reading Time: 6 minutes

Without a doubt, the foods we eat will impact autoimmunity. However, that doesn’t mean foods can’t still be delicious and enjoyable. Luckily, there are so many healthy, autoimmune-friendly food alternatives to common inflammatory ingredients. And it just so happens that one of my favorite things to do is help individuals take the stress out of what to eat and find alternatives they love! 


Essentially, the foods we eat have the power to harm or heal the body. All the foods we consume, from morning to night, affect every function in the body, including: metabolism, hormones, digestion, brain function, energy production, and more. The immune system, and thus autoimmunity, is no exception. 

In the case of autoimmunity, diet and nutrition plays a huge role. It’s therefore important to avoid inflammatory foods and those that you are sensitive or allergic to. Unfortunately, these foods naturally create an inflammatory response in the body, which also prevents healing from taking place and often causes unwanted symptoms. Inflammation, which breeds leaky gut, is the root of autoimmunity. And it’s with the right kinds of food that you can strategically reduce inflammation, heal the gut, and reverse your autoimmune symptoms once and for all. 


Inflammatory foods can easily trigger autoimmune flares. The most common foods that cause inflammation include:

Common autoimmune triggers

For those with Celiac Disease and Non-Celiac Gluten Sensitivity (NCGS), they should immediately eliminate gluten from the diet. Truthfully, even if you don’t have Celiac Disease or NCGS, adopting a gluten-free diet can be extremely beneficial in the healing journey. Gluten is often present in common foods, like pasta, bread, cakes, and cookies. Gluten creates large gaps in the gut lining, leading to a gut dysfunction called “leaky gut.” As a result, inflammation sky rockets and healing is difficult.


Pseudograins, like quinoa, buckwheat, and oats, are naturally gluten free. However, these kinds of grains mimic gluten in the body, eliciting a very similar response. As inflammation increases, the gut lining is further damaged and healing is nearly impossible.


Soy is a very common ingredient in many foods today, including soy sauce, dressing, marinades, soy protein, soy milk, and more. It can be inflammatory to all, especially those with autoimmunity, due to their high content of phytoestrogens and antinutrients. Phytoestrogens mimic estrogen in the body, naturally leading to estrogen dominance and hormonal imbalances. Antinutrients, like lectins, are also very hard-to-digest and create nutrient deficiencies.


Some foods affect thyroid function when eaten excessively. These are called goitrogens. Goitrogenic foods can have a severe impact, sometimes leading to Hashimoto’s or Grave’s Disease. When eaten in large amounts, goitrogens, like brussel sprouts, broccoli, and cauliflower, and soy-based foods decrease the production of thyroid hormones. They block iodine from entering the thyroid, interfere with thyroid peroxidase enzyme, reduce thyroid stimulating hormones, and ultimately, lead to thyroid dysfunction. Again, note that this occurs when these foods are eaten in extreme amounts or if you suffer with a thyroid condition. 

Conventional Dairy

Dairy that is processed and pasteurized is highly inflammatory, especially to those with autoimmune disease. For some, it’s best to avoid dairy altogether. However, for others, small amounts of A1 dairy are tolerated. A1 dairy, as opposed to A2 dairy, doesn’t create the same inflammation and digestive upset.

Best dairy options

Unsurprisingly, coffee contains high amounts of caffeine. This excess caffeine leads to a chronic stress response in the body. But, that’s not all. It’s also a common source of mycotoxins, which can cause toxicity issues. 


Unfortunately, many chocolate products are highly processed and contain higher amounts of phytic acid and mycotoxins. As a result, the absorption of many essential nutrients, like zinc, calcium, magnesium, iron, and copper is inhibited. This can be triggering to those with autoimmunity.


Despite the many inflammatory foods around today, there are so many delicious, nutritious, and anti-inflammatory alternatives. My favorite autoimmune-friendly food alternatives include:

Delicious food alternatives for autoimmunity

Opposed to traditional gluten-filled pasta, cassava or chickpea pasta is a great alternative. These alternatives also contain other fresh ingredients that encourage healing.

Brands: Jovial grain free varieties or Capellos


Most tortillas are made with traditional flour or corn, leading to digestive upset, headaches, and other chronic symptoms. However, wraps made with coconut or cassava flour are much less inflammatory.

Brands: Siete and The Real Coconut


Flour, made from gluten-filled wheat, is not an option for those with autoimmunity. However, there are plenty of flour alternatives available today, including almond, coconut, or cassava flour. These flours are also rich in fiber, antioxidants, and prebiotics.

Brands: Bob’s Red Mill GF blends or Otto’s Cassava


Cereal is a childhood favorite treat for many. Unfortunately, all conventional cereals are made with fortified flours, chemicals, and food dyes. Instead, look for cereals that are grain and sugar free.

Brands: LoveBird or One Degree Organics 

Soy Sauce

Soy sauce is a necessity in the kitchen for many. While it has a distinct flavor for many asian or mexican dishes, coconut aminos offer a similar taste without the estrogenic effects of soy. 

Brand: Coconut Secret

The benefits of coconut aminos, an AIP food alternative for soy sauce
Dairy-Free Milk

Given the inflammatory nature of conventional milk, it’s not an option for many who have autoimmunity or are lactose-intolerant. Instead, look for coconut or cashew milk that is free from added gums and fillers. 

Brands: Native Forest or Malk

Yogurt or Kefir

Yogurt is a great source of probiotics and can be extremely beneficial for those with autoimmune disease. Instead of dairy, opt for dairy-free alternatives, like those made with coconut milk. 

Brands: Coyo or Anitas.


Similar to all dairy products, cow cheese naturally creates an inflammatory response in the body. However, goat cheese isn’t as hard to digest and can be a great option. Or, try vegan cheese for a delicious and healthy alternative.

Brands: Saputo or Miyokos Creamery


There is good news for those who just can’t give up their morning cup of coffee. Look for coffee that is made from organic beans and is tested for mold and mycotoxins.

Brands: Purity Coffee


Many chocolate bars, chips, and candies are made with soy lecithin, added sugars, milk, and other inflammatory ingredients. Instead, opt for dark chocolate that is 70% chocolate or above without added gums or fillers. 

Brands: Hu Chocolate or Alter Eco


Butter is a great source of stable fats for cooking, however, many with autoimmunity cannot tolerate it. Ghee, or clarified butter, removes the dairy component of dairy. It’s a great option for those who can’t consume butter!

Brand: 4th & Heart, Kerry Gold

Refined Sugar 

Refined, white sugar is inflammatory and also has carcinogenic effects on the body. Alternatively, honey that is raw and local has minimal effects on blood sugar and offers antioxidant properties. High quality maple syrup is also a healthier option!

Brands: Any raw, local honey or Coomb’s Family Farm maple syrup


Eating to heal autoimmunity, instead of exacerbating it, can be challenging and confusing at first. To help you conquer the art of autoimmune-friendly nutrition and food alternatives, I created a customizable Monthly Meal Plan Subscription. The meal plan provides many gut and autoimmune-friendly recipes using some of these favorite alternatives. Learn more about this effortless approach to autoimmunity nutrition, here!

Best food alternatives for autoimmunity

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"When it comes to balancing our body, healing the gut, reversing autoimmunity, and achieving optimal health—we are a lot like a car that won’t run right. In order to fix the problem once and for all instead of relying on jumper cables, we must get underneath the hood, run the diagnostics, and replace the battery so that it runs good as new."

-Nikki Yelton, RD

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