Autoimmune Paleo Diet for Autoimmune & Chronic Disease

There are numerous dietary protocols that can help a person with Chronic Disease feel better. In some cases, a dietary approach can produce a complete remission of the condition!
For me, as a clinician, the goal of the approach is to help your body reset, nourish itself, and reduce inflammation caused by reactive foods — as well as to help you reconnect to an intuitive way of eating, where (eventually) you will naturally select foods that make you feel better, and avoid those that make you feel worse.
While I don’t believe in a “one size fits all” diet, I have seen versions of the Paleo type diet work wonders for many people with Chronic Disease, as it eliminates many of the foods that are most problematic — including gluten and dairy. However, some people with autoimmune conditions will need to take their diet a step further. In such cases, the Autoimmune Paleo (AIP) diet has been shown to be highly effective for many.
The Origins of the Paleo Diet
First, let’s talk about the Paleo diet, which is the diet from which the Autoimmune Paleo (AIP) diet originates. Many people, even those not diagnosed with Chronic Disease, are aware of the benefits of the Paleo diet. It has helped countless people feel better from a wide range of symptoms: fatigue, brain fog, joint pain, gas, and bloating, to name a few. In the case of Chronic Disease, the traditional Paleo diet has even helped many people lower — or completely eradicate — their symptoms and antibodies.
For those of you who have tried going Paleo but have not seen significant improvement, I want you to know there are additional steps you can take that will give you the power to take back your health!
The traditional Paleo diet is a classic elimination diet that focuses on omitting foods people are commonly sensitive to in an effort to lower inflammation.
As you may know, the Paleo diet eliminates all grains, legumes, soy, and processed foods. The focus is on replacing the foods you take out of your diet with other nutrient-dense foods, such as organic or grass-fed meats, wild-caught fish, organic vegetables and fruits, nuts, seeds, eggs from pasture-raised hens, and (depending on who you ask) dairy.
The Paleo diet is certainly a great start, but it is not always enough to address every case of Chronic Disease. Often, we need to peel back more layers of that onion! The good news is, with each new diet, supplement, or treatment that you try, you are finding out how your body responds to different external factors. Each case of Chronic Disease is unique, and many of us have additional food sensitivities that are deregulating our immune system. People with Hashimoto’s often have sensitivities to a wide range of foods — particularly to gluten, dairy and soy — which are all omitted on the traditional Paleo diet.
Anecdotally, the Paleo diet is said to have been introduced in the 1970’s with the book The Stone Age Diet by Walter Voegtlin, but it has significantly gained in popularity over the past ten years. Since then, countless resources such as cookbooks, websites, and articles have been created that include recipes ready for you to use. I’m sure many of you have seen these resources at your local bookstore, your go-to health food store, and even at Costco. It’s a very exciting time to be on a Paleo diet!
If the Traditional Paleo Diet Does Not Improve All My Symptoms, What’s Next?
Now that you understand Paleo, let’s talk about the AIP diet.
The creation of the AIP diet has been attributed to Loren Cordain, a scientist who discovered that certain foods can sometimes trigger inflammation in people with chronic disease and autoimmune disease. It was further popularized by Paleo authors such as Robb Wolf in The Paleo Solution, and Sarah Ballantyne (also known as The Paleo Mom) in her book, The Paleo Approach.
The goal of the AIP diet is to heal leaky gut by removing commonly problematic foods, thereby reducing inflammation in the body and healing autoimmune disease.
I have seen many of my clients find almost complete relief from their symptoms by implementing the AIP diet into their lifestyle changes. The symptoms that many find relief of include joint pain, muscle aches, fatigue, bloating, diarrhea, brain fog, tinnitus, skin rashes, as well as decreased food sensitivities. Even those who do not recover completely will often experience significant improvement. You have nothing to lose (except for symptoms!), and everything to gain by considering the AIP diet.
Will I Feel Better Right Away on AIP?
Please note that there is often a short transition/withdrawal period before you start feeling better on the AIP diet, especially if you are new to coming off gluten, dairy, and processed foods.
Research suggests that casomorphins (from the dairy protein casein) and gliadorphins (from gluten, a protein found in wheat) can bind our “feel good” endorphin receptors, much like the morphine found in addictive drugs can.
This has led some people to say that these foods are as addictive as heroin and other drugs (which also bind our endorphin receptors). While I think this is an exaggeration, I have seen people experience withdrawal-like symptoms, including brain fog, irritability, cravings, fatigue, and headaches, after quitting gluten, dairy, and sugar while they were adhering to the Autoimmune Paleo diet.
The good thing is, once these inflammatory foods have been eliminated, you will start to feel better. You can expect to see results within 30-90 days of implementing the AIP diet, although it may take longer. If you do not see results in 30 days, eliminate mammalian meat and use fish as your main protein source. Then, you can start to systematically reintroduce certain foods one by one. This allows you to create a diet for the long term that is tailor-made for you.
This process will allow you to be more in touch with what does — and doesn’t — work for you.
However, while the Autoimmune Paleo diet has helped many people with Chronic Disease and autoimmune conditions get better, it can be quite difficult to implement. As a pharmacist, I see this daily: many people know what they need to do to get better, but just don’t know how to get started.
If you’ve been eating the standard Western diet for most of your life, starting a dietary protocol like the AIP can be extremely intimidating. Though you may eventually end up “going AIP,” it’s okay to take baby steps and begin with going gluten free, then move on to going dairy and soy free.
I encourage you to remove one food group at a time, if that makes you feel more at ease with the transition. Committing to a 100 percent gluten-free diet is an important first step.
I know that some of you, however, love taking action and will dive right in and immediately begin your healing journey with the AIP! However, many of you will find the AIP diet difficult to adhere to at first. We all have different needs, motivations, and challenges, and I encourage you to honor your individuality and listen to your body.
The Autoimmune Paleo Diet Guidelines
At this point you’re probably wondering where to begin with the AIP diet. Let’s start by going over the lists of foods to avoid and those to focus on with the diet.
Foods to Be Avoided on the AIP Diet
When you do decide to start the AIP diet, you’ll notice that, in addition to following the Paleo diet guidelines of removing gluten/soy/dairy/grains/nightshades/legumes/processed foods, it also removes additional foods that are known to cause inflammation in many people. Here’s the full list of foods to be avoided on the AIP:

  • Gluten
  • Grains (including corn, quinoa, buckwheat, and rice)
  • Dairy
  • Eggs
  • Soy
  • Alcohol
  • Caffeine
  • Beans and legumes
  • Nightshades – tomatoes, potatoes (except for sweet potatoes), eggplant, peppers, goji berries, ashwagandha (herb that helps balance adrenals and thyroid), paprika and other nightshade spices
  • Seaweed and other sea vegetables*
  • Sugars (including honey, maple syrup, and agave)
  • Canned foods, processed foods, coffee
  • High glycemic index foods
  • All nuts and seeds (except coconut)

*While seaweed and sea veggies aren’t traditionally removed on the AIP diet, I recommend avoiding them because of their high iodine content, which may exacerbate autoimmune thyroid disease.
Foods to Be Included on the AIP Diet

  • Organic vegetables (except nightshades and legumes)
  • Fermented foods (sauerkraut, nightshade free kimchi, coconut kefir, kombucha, fermented vegetables, and jams)
  • Organic and grass-fed meats
  • Organic and grass-fed organ meats
  • Wild-caught fish
  • Fats and oils
  • Low-glycemic organic fruits
  • Coconut (including coconut milk and coconut oil)
  • Herbs and spices
  • Hydrolyzed beef protein
  • Sweet potatoes

Recommended Best Practices
While the AIP diet can seem a bit intimidating, if you follow a few rules and stick to the list of allowed foods, you will find that you quickly adjust to the diet, and it’ll become second nature:

  • Limit fruits to 1-2 servings per day and make sure they are low on the glycemic index (a ranking of how fast carbohydrates are digested)
  • Include 6-8 servings of vegetables per day
  • Aim for 80 percent vegetables, and 20 percent meat or fish in each meal
  • Focus on sauces, dips, and broths
  • Incorporate plenty of fats and oils (coconut oil, duck fat, beef tallow, avocado oil, olive oil), cooked at the appropriate temperature
  • Don’t eat on the run, and make sure to chew your food thoroughly
  • Learn to ferment your own vegetables
  • Drink plenty of filtered water
  • Don’t forget to check supplement labels to make sure they are free of non-compliant ingredients. For your medication, check Gluten Free

An Example Day’s Worth of Meals
Here are some meal ideas:

  • Bacon
  • Steamed spinach with olive oil
  • Avocado
  • Fermented cabbage (from farmer)
  • Fermented cucumbers (my recipe)


  • Butternut squash chili (Remember, batch cooking is your friend 🙂
  • Fresh Swiss chard with lemon, sea salt, and olive oil


  • Coconut crusted trout


  • Mineral water with lemon and lime or, for the occasional treat, add a few berries
  • Herbal teas are a great choice on an AIP diet

Need a Snack?

  • Sip on some homemade bone broth, enjoy a green smoothie, a slice of avocado with a squeeze of lime and sea salt (yum!), or make some savory sweet potato chips

What If AIP Is Not Enough?
The Autoimmune Paleo diet is meant to be short term. As I mentioned earlier, the goal is to reduce body inflammation and allow the gut a chance to heal. These variations in diet give you the power to improve how you feel and isolate your root causes.
If, however, AIP doesn’t resolve many of your symptoms after 90 days of following it, you may have to go a step further and incorporate a rotation diet, a low-histamine diet, or low-oxalate diet.
If, after 90 days, you are still having gut issues, it may be a good time to test for parasites and other gut infections, as well as SIBO.
Food & Pantry Items to Help You Stock an AIP-friendly Kitchen

  • US Wellness Meats
  • Vital Choice Wild Seafood
  • Desert Farms Camel Milk
  • Paleo On The Go
  • The Flavor Chef (The Brothery) – Be sure to look for the products marked as AIP and use “thyroid10” for your special discount!
  • Thrive Market

Some Helpful Cooking Tools to Make AIP Life Easier

The Takeaway
While there is no one-size-fits-all diet, the Autoimmune Paleo diet has helped many people with Chronic Disease and Autoimmune disorders. If you find you are stuck in a rut with your symptoms, trying this diet for a period of time may be the solution you need to find relief.
Starting an AIP diet may seem intimidating at first, but for many people with Chronic Disease, the benefits far outweigh the inconveniences. Once you get going and see the progress you make, you will not want to turn back!

  1. Abbott RD, Sadowski A, Alt A3. Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto’s Thyroiditis. Cureus. 2019 Apr 27;11(4):e4556. doi: 10.7759/cureus.4556.

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