Beginner's Guide to the Autoimmune Protocol




There’s a lot of information out there when it comes to what we should and shouldn’t be eating. Between low carb, gluten-free, paleo, vegan, keto, etc., it can be hard to sort out!

While I believe there is no ‘one size fits all’ when it comes to diet, I do think we all need to be emphasizing whole, unprocessed foods and cutting out the processed junk as much as possible! In my holistic nutrition consulting practice, I customize each client’s nutrition plan to him/her based on bio-individuality. Factors I consider are things like genetics, ethical/spiritual beliefs, health conditions, activity levels and, of course, personal wellness goals.

For my clients with autoimmune disorders, I generally recommend and guide them through implementing the Autoimmune Protocol (AIP) diet. Before we get into what AIP entails, let’s some basics straight…

What is autoimmunity?

Autoimmune problems arise when your immune system mistakenly identifies certain tissues in your body as invaders rather than "self." When this happens, the immune system releases chemicals that cause a cascade of destructive inflammation. The research of Dr. Alessio Fasano has revolutionized the way we understand autoimmune disease as a three-legged stool. The three legs are genetic predisposition, a triggering event (such as toxin exposure or a chronic infection) and intestinal permeability.

There are more than 80 types of autoimmune disorders and more are being discovered all the time. To be diagnosed with most autoimmune diseases, the immune system has to destroy a significant amount of tissue to be officially diagnosed. In multiple sclerosis, for instance, the central nervous system comes under attack. In rheumatoid arthritis, it's the joints. In Crohn's disease and celiac disease, it's the gastrointestinal tract. In Hashimoto thyroiditis and Graves, it’s the thyroid.

For months and even years, the self-tissue attack can occur silently until a full-blown autoimmune disease develops. But here’s the kicker – these diseases do not happen overnight! The diagnosis happens at the end stage, but there is destruction happening over time and there is a lot we can do to stop it! Stanford research estimates that about 77 percent of the immune system is determined by things we can actually control (lifestyle factors like diet, exercise, and stress), with the remainder due to genetics.

So whether you have been diagnosed with an autoimmune disease or are somewhere on the “autoimmune spectrum” (where you may have significant symptoms but are still not conventionally diagnosable), you can be eating and living your life in a way that calms your immune system and douses the fire of inflammation on a daily basis! In order to treat, prevent and reverse an autoimmune disease, you’ll need to get inflammation down and your immune system under control.

So how do we do this?

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The healing power of food

As Hippocrates, the father of medicine, said “Let food be thy medicine, and medicine by thy food.” This couldn’t be truer with regards to treating autoimmunity as diet plays a big part in worsening or treating autoimmune conditions. Why? Because when you eat pro-inflammatory foods (for instance, sugar and white flour), you exacerbate inflammation, the core feature of all autoimmune disorders. Unhealthy foods can also worsen intestinal permeability ("leaky" gut), throw your hormones out of balance, and lead to nutritional deficiencies — all of which can worsen the symptoms of an autoimmune disease.

Conversely, by eating healing whole foods, you can reduce inflammation, balance your hormones, foster healthy intestinal flora that help heal leaky gut, and correct nutritional deficiencies. When you do this, you can often put your condition into remission.

The Autoimmune protocol (AIP) is a variation of the Paleo diet that specifically addresses inflammation and leaky gut.

Autoimmune Protocol

My protocol for clients with autoimmune conditions begins with a 30-day nutrition reset. During this time, I recommend eating a diet completely free of the following foods (100% compliance is really important):

  • Gluten and Grains (Corn, Wheat, Millet, Buckwheat, Quinoa, Rice, Sorghum, Amaranth, Rye, Spelt, Teff, Kamut, Oats, etc)
  • Dairy (milk, cheese, yogurt, ice cream, etc.)
  • Beans/Legumes (this includes all beans like chickpeas, peas, kidney beans, pinto beans, black beans, etc. as well as lentils and soy in all its forms)
  • Nuts (peanuts, walnuts, almonds, macadamia nuts, pecans, pine nuts, brazil nuts, etc.)
  • Seeds (flax, chia, pumpkin, sunflower, sesame)
  • Eggs - While eggs are a superfood, a significant number of people react badly to them — especially to the whites. Here's a good article on this topic.
  • Nightshades (tomatoes, potatoes (except for sweet potatoes), eggplant, peppers, okra, goji berries, paprika, chili powder, cayenne pepper, red pepper flakes)
  • Algae (spirulina, chlorella, etc.)
  • Vegetable oils (canola, cottonseed, corn, soy, peanut, sunflower, safflower) and trans fats
  • Chocolate and cocoa
  • Sugar, stevia and artificial sweeteners (Splenda, Equal, Sweet N Low)
  • Alcohol
  • Coffee
  • Processed foods (additives, preservatives, emulsifiers, thickeners and colorings)

Instead, eating a diet of healing anti-inflammatory foods, including:

Recommended Best Practices

  • Include 6-8 servings of vegetables per day
  • Limit fruits to 1-2 servings or or 15-20 grams of fructose per day
  • Incorporate plenty of fats and oils
  • Drink plenty of filtered water

Example Day on the AIP Diet


  • Savory – BF Hash
  • Organic nitrate-free bacon
  • Sauteed kale in olive oil
  • Avocado
  • Sauerkraut

Sweet - Smoothie

  • Collagen peptides
  • Avocado
  • Spinach
  • Berries
  • Cinnamon
  • Ginger
  • Coconut milk or water


  • Salad with shredded chicken, mixed greens, cucumbers, carrots, radishes, spring onions, olives, avocado and a simple lemon juice and olive oil dressing
  • Or Dinner leftovers


  • Coconut crusted cod with roasted broccolini and baked sweet potato
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  • Plain filtered water
  • Mineral water with lemon and lime
  • Herbal teas

Need a Snack?

If you feel too overwhelmed by jumping straight to AIP, I recommend taking baby steps and slowly transitioning your diet. Start with a 100% gluten free diet. Once you get the hang of that, cut dairy and soy. From there, you can follow the Paleo diet. By this stage, you’ll likely already begin noticing positive health changes, such as reduction in joint pain, weight loss, feeling more energized, etc. Then when you’re ready to go whole hog, do the AIP Diet for 30 days.

After a month on AIP, I recommend systematically reintroducing restricted 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 will be more in touch with what does—and doesn’t—work for your body.

How to “challenge” the restricted foods:

You will reintroduce a single food category (i.e. dairy) for three days only. Two servings per day. Monitor your symptoms for a full week. The last 4 days of the week, look for delayed onset symptoms. For example, you might decide to reintroduce dairy* on a Monday. Monday through Wednesday, you could eat some organic, whole milk, plain yogurt, kefir, cheese, or drink a small glass of milk at two of your meals those days. Resume your elimination diet from Thursday through Sunday and monitor any abnormal reactions. If you do not have any observable symptoms, you may try introducing a new food (i.e. eggs) on the following Monday.  Continue this process for the following weeks until you have reintroduced all food categories that you would like to consider adding back into your nutrition plan. If you have no symptoms, you are welcome to include that food category back into diet ongoing.  

*I recommend introducing goat’s, sheep’s and cow’s dairy separately.

The key to this approach is paying attention to how you are feeling and recording any symptoms you experience in a food journal. Look out for the following symptoms:

  • Headaches
  • Bloating, gas and/or digestive upset
  • Rashes / hives
  • Fatigue / lethargy
  • Joint pain
  • Muscle aches
  • Racing heartbeat
  • Numbness
  • Mood swings
  • Hot flashes
  • Sleep disturbances
  • Brain fog
  • Any suddenly occurring symptom like nausea, depression, or anxiety

I recommend keeping a food journal during this process. In your journal, record which food you’re challenging, any symptoms you experience and whether your reaction is mild, moderate or severe. At the front or back of the journal, you can make a list of the foods that you feel good eating, and a separate list for the foods which relate to symptoms in your body. At the end of the challenge, you should be able to freely eat all foods that you did not have a reaction to.

While this process of testing for food sensitivities takes some patience, reducing inflammation, healing your gut and feeling better is so worth it! The good news is, once your body has healed more deeply over time, you may be able to reintroduce some foods in moderation that were previously causing problems.

After completing the 30-day reset and subsequent reintroduction phase of AIP, evaluate where you are at on the autoimmunity spectrum. How are you feeling? Have your symptoms improved? If your diet was the root cause of your inflammation, it is likely that many of your symptoms have vanished. It is also possible that there are other factors that need your attention in order to work your way down the spectrum and reverse your condition. You may consider working with a holistic health practitioner to repair your gut, eliminate toxins in your life, heal any infections and manage your stress. Just remember that you have the power to regain optimal health by addressing the root causes that led to your inflammation and autoimmunity. Try to be kind and gentle with yourself through the process!