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Autoimmune Protocol AIP Elimination Phase

Autoimmune Protocol AIP Elimination Phase

Autoimmune Protocol AIP Elimination Phase

The autoimmune protocol (AIP) is a way of eating and living specifically designed to help those of us with autoimmune disease find relief from our symptoms.

The nutrition side of the autoimmune protocol includes three phases:  the elimination phase, the reintroduction phase, and the maintenance phase.

I go over the ins and outs of the elimination phase in this article.  You can read about the reintroduction phase here.

What are the benefits of the autoimmune protocol (AIP) elimination phase?

The autoimmune protocol, including both the nutrition and lifestyle guidelines, is designed to minimize autoimmune symptoms and maximize immune function.

The autoimmune protocol is not a one size fits all way of eating and living.  While many autoimmune disease sufferers find relief from their symptoms through the AIP, others may need to trouble shoot or make adjustments based on bio-individual needs.  Also, the amount of time spent in each phase of the AIP will vary.

Further, it is important to work with a medical team to address root causes of autoimmunity, monitor labs, adjust medication as necessary, and so on.  A functional medical doctor can be instrumental.  To learn more about functional medicine or to locate a functional medical doctor near you, click here.

For the science behind why the autoimmune protocol works as far as what is going on in the body with autoimmune disease and why certain foods are eliminated for a time, I recommend The Paleo Approach by Dr. Sarah Ballantyne.

The Importance of Bio-individuality

All information shared is to be used as a general guideline. Please remember everyone is different. What works best for one person will look differently than what works best for another person.

Learn to listen to your body, and find what works best for you.

AIP Elimination Phase Basics

In the elimination phase of the autoimmune protocol, foods that trigger an immune response are temporarily eliminated to give the immune system a chance to rest.

Many autoimmune disease sufferers find relief from their autoimmune symptoms during the elimination phase.  While many people experience a gradual improvement in their symptoms, some find quicker relief.

The amount of time spent in the elimination phase varies, and depends on the individual.  Typically, the elimination phase lasts a minimum of 30-90 days.  Although some stay on the elimination phase much longer, it is not designed to be lifelong.

AIP Addresses Four Key Areas

Nutrient Density

Every system in the body, including the immune system requires a variety of vitamins, minerals, antioxidants, essential fatty acids, and amino acids to properly function. Micronutrient deficiencies as well as imbalances contribute to autoimmune disease. Nutrients are necessary for healing and repair.  One of the goals of the autoimmune protocol is to flood the body with a variety of nutrients essential for healing and restoring.

Gut Health

There is a strong correlation between gut health and immune function. Gut dysbiosis and leaky gut contribute to the development of autoimmune disease. AIP includes foods that help restore gut health, while excluding foods that damage or irritate the lining of the gut.

Hormone Regulation

A variety of hormones that interact with the immune system are impacted by the foods we eat, how much we eat, as well as when we eat. As a result, the immune system can be impacted by dysregulated hormones. AIP is designed to help with hormone regulation.

Immune System Regulation

What helps immune regulation? Improving gut health, consuming a variety of micronutrients that the immune system requires to properly function, and healthy hormone regulation. Both AIP diet and lifestyle are designed to improve immune system regulation and in turn help reduce autoimmune symptoms.


AIP Elimination Phase Foods to Include

One of the goals of the autoimmune protocol (AIP) is to flood the body with nutrients, so the foods to include are just as important as the foods to exclude.

Source the best quality ingredients you can (use the dirty dozen and clean fifteen list as needed and cross reference it with the AIP list of foods to include and exclude which you can download and print for free here).

Remember:  the more variety of foods and nutrients you include, the better.

Quality Meats

Quality Meats

Grass-fed, pasture-raised, wild as much as possible.

Be mindful to eat poultry in moderation due to high omega-6 content, unless you eat fish often.

Fish and Shellfish

Ideally try to eat wild caught if possible, but farmed is okay.

Ideally aim for at least 3 times per week.

Organ Meat and Offal

Ideally aim for at least 5 times per week.

If you cannot stomach organ meat yet, I recommend beef liver capsules – 2 capsules 2x per day depending on the brand.  

Healthy Fats

Healthy Fats

  • pasture-raised/grass-fed animal fats (rendered or as part of your meat)
  • fatty fish
  • olive oil
  • avocado oil
  • coconut oil
  • palm oil (not palm kernel)


Vegetables of all kinds (except nightshades): at least 8+ servings daily and as much variety as possible. Make it a game and see how many colors you can eat!

Leafy Greens

  • lettuce
  • spinach
  • kale
  • collards
  • celery leaves
  • chard
  • and more!


  • broccoli
  • cabbage
  • kale
  • turnips
  • arugula
  • cauliflower
  • brussels sprouts
  • watercress
  • mustard greens
  • and more!

Roots, Tubers, & Winter Squash

  • sweet potato
  • cassava
  • parsnip
  • beets
  • fennel
  • carrots
  • rutabaga
  • turnip
  • acorn squash
  • spaghetti squash
  • and more!

Onion Family

  • yellow onions
  • red onions
  • sweet onions
  • green onions
  • leek
  • garlic
  • and more!

Sea Vegetables

Note: be sure to exclude algae like chlorella and spirulina. Both are immune stimulators.

Check your supplements for both ingredients.


As well as other edible fungi.

Bonus: mushrooms are a gut microbiome super food!

Herbs and Spices

Herbs & Spices

Except seed based spices.

Probiotic & Fermented Foods

Probiotic & Fermented Foods

  • fermented vegetables or fruit like sauerkraut
  • kombucha
  • water kefir
  • coconut milk kefir
  • coconut milk yogurt
  • and more!

Note:  if you purchase any of these items from the store (versus homemade) make sure they do not contain any non AIP ingredients.

Glycine-Rich Foods

Glycine-Rich Foods

Anything with connective tissue, joints or skin, organ meat, and bone broth.

Bone broth is easy and inexpensive to make!

Gut Microbiome Superfoods

Gut Microbiome Superfoods

  • high-fiber and phytonutrient fruits and vegetables
  • cruciferous vegetables
  • mushrooms
  • roots
  • tubers
  • leafy greens
  • berries
  • apple family
  • citrus
  • EVOO
  • fish
  • shellfish
  • honey
  • fermented foods
  • bone broth
  • and more!


All Kinds of Fruit

Ideally it’s best to aim to keep fructose intake between 10g and 40g daily when starting the AIP.   Keeping in mind that 20g is probably optimal – learn to listen to your body and find what feels best.  Make adjustments accordingly.

Cronometer is a great free app and website for tracking nutrition.

AIP Elimination Phase Foods to Exclude

See detailed list of foods to exclude here.

  • grains
  • legumes
  • dairy
  • eggs
  • nuts (including nut butters, flours and oils)
  • seeds (including seed oil, cocoa, coffee and seed-based spices)
  • nightshades (potatoes- except sweet potatoes, tomatoes, eggplants, sweet and hot peppers, cayenne, red pepper, tomatillos, goji berries, and more, also spices derived from peppers, including paprika)
  • refined and processed sugars
  • alcohol
  • NSAIDS (like aspirin and ibuprofen)
  • non-nutritive sweeteners (even stevia and monk fruit)
  • refined and processed oils
  • emulsifiers, thickeners, and other food additives
  • potential gluten cross-reactive foods (many have already been mentioned here but click here for more information)

Note:  Be mindful of hidden ingredients in foods.  The easiest way to avoid hidden ingredients is to stick to real, whole, unprocessed foods.

AIP Elimination Phase Foods to Eat in Moderation

  • fructose (from fruits and starchy vegetables, aiming for between 10g and 40g daily)
  • salt (be mindful to use only unrefined salt such as Himalayan pink salt or Celtic gray salt)
  • high glycemic load fruits and vegetables (for example, dried fruit, plantain, and taro root)
  • omega 6 polyunsaturated fatty acid-rich foods (for example, poultry and fatty cuts of industrially produced meat)
  • black or green tea (up to 3-4 cups per day is okay for most people)
  • coconut (as well as coconut products like coconut flour, coconut milk, etc.; many coconut milks have additives that are not AIP like guar gum – look for a coconut milk with no added gums or ingredients)
  • natural sugars (honey and blackstrap molasses are the best choice / pay attention to how you feel when consuming natural sugars)
  • saturated fat (a general AIP elimination phase rule of thumb is to aim for 10-15% of total calories)

AIP Elimination Phase:  Does the 80/20 Rule Work?

The 80/20 rule is basically that you eat healthy or according to a certain diet 80% of the time, and then eat whatever you want the other 20% of the time.

Generally speaking (remember bio-individuality), AIP elimination phase is not an 80/20 rule kind of eating plan. It is a temporary healing protocol / elimination diet to strictly follow 100% of the time for a minimum of 30 days. The goal is to remove foods that are known to trigger the immune system.

With that said, you do not have to go ALL in on AIP elimination phase if that feels overwhelming for you. There are different ways to approach and start AIP, and it’s important to find what works best for you in your life.  If you need some help and support to start, restart, or learn more about the AIP, I’d love for you to join my AIP online group coaching program (you can learn more here).

Try to think of the time you spend in AIP elimination phase as an investment in your health and wellness journey.

“Can I REALLY do this?!”

Please know if the AIP elimination phase feels overwhelming or difficult, you are not alone.

I felt the same way when I started the AIP.  It’s been quite the journey, and although it’s one of the hardest things I’ve done, it’s also been truly one of the most rewarded.  You can read more about my AIP journey here.

I know this life with autoimmune disease is tough stuff.

It can feel so lonely, frustrating, and fearful.

It never ceases to amaze me how important mindset and lifestyle is when it comes to successfully navigating the AIP, for both myself as well as for my clients and fellow AIPers.

If you find yourself continually struggling to start AIP elimination phase, remember to consider mindset and lifestyle and perhaps start there instead.  There’s no right or wrong way to start AIP, and both mindset and lifestyle are game changers.

Please know I am cheering you on and sending you loads of love and support from one autoimmune warrior to another…you got this!

Big hugs!



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