What is the Paleo Autoimmune Protocol (AIP)?


The Paleo Autoimmune Protocol, sometimes referred to as AIP, is a therapeutic elimination diet used to help heal gut dysfunction and the immune system. The protocol uses both diet and lifestyle strategies to not only heal the body, but to also identify triggers that cause autoimmune flare-ups or unwanted symptoms. 


What is the Paleo Autoimmune Protocol (AIP)?

The Paleo Autoimmune Protocol, often shortened to autoimmune paleo or AIP uses both diet and lifestyle as a strategy to help reduce inflammation and relieve symptoms of autoimmune diseases. The protocol is geared towards restoring the integrity of the gut through healing the intestinal mucosa and supporting low inflammation in the body that causes autoimmune flare-ups.

People who follow the AIP diet eliminate some foods permanently and remove certain foods for 4-12 weeks. Some people require longer periods of elimination for healing. After the elimination phase, foods are slowly reintroduced to see if a food reaction occurs. Through this process, people decipher which foods should be excluded from their diet long-term. The Autoimmune Protocol also emphasizes lifestyle and the importance of sleep, physical activity, rest, and stress management.

Who Can Benefit from AIP?

The AIP diet is appropriate for those with autoimmune disease. Autoimmune disease is a condition where the body cannot tell the difference between healthy tissue and foreign invaders. As a result, our immune system, the part of our body responsible for protecting us from invading microorganisms, actually turns against us and attacks our proteins, cells, and tissues. For example, Celiac Disease is an autoimmune disease triggered by consuming gluten, a protein found in wheat, barley and rye. When people with celiac (like myself) eat foods containing gluten, their immune system responds by damaging the finger-like villi of the small intestine.

Unfortunately, a majority of autoimmune diseases go undiagnosed and although they can never be cured, proper diet and lifestyle habits such as AIP can enable remission. There are over 100 autoimmune diseases, some of which include:

  • Celiac disease

  • Crohn’s disease

  • Fibromyalgia

  • Hashimoto’s thyroiditis

  • Lupus

  • Lyme disease

  • Rheumatoid arthritis

  • Scleroderma

AIP may benefit people with common health issues associated with autoimmune disorders such as chronic fatigue syndrome, eczema, fibromyalgia, and polycystic ovary syndrome (PCOS), as well as anyone with signs or symptoms off autoimmunity, such as adrenal fatigue, hormonal imbalances, parasites, SIBO, liver congestion, insulin resistance and blood sugar problems. 

emily morrow autoimmune aip stress.jpg

Symptoms of Autoimmunity Include:

  • Fatigue, aches or pains

  • Stomach ache, heartburn, nausea, constipation, diarrhea, change in frequency of bowel movements

  • Gas, bloating

  • Mood swings, such as anxiety or depression

  • Difficulty losing weight

  • Headaches, migraines, dizziness or lightheadedness

  • Hormonal imbalances

  • Reduced energy, fatigue, or energy dips in the afternoon, or a second wind in the late evening that makes it hard to go to bed at a good time

  • Trouble falling asleep, staying asleep, or not feeling well rested in the morning

  • Allergies

  • Skin issues, such as acne, eczema or rashes

  • Anxiety, difficulty managing stress

Each person who decides to try the AIP diet should work with a practitioner to determine if they might need additional specialization such as a low histamine or low FODMAP protocol. This may include functional blood chemistry, saliva hormone testing, saliva adrenal testing, stool testing, genetic testing and evaluation and antibody testing.

Foods to Avoid on AIP

AIP is an elimination diet, meaning it is not meant to last forever. The protocol requires a temporary elimination  of known or suspected gut irritant foods, such as eggs, dairy, nuts, seeds, nightshades, too much fructose, food additives, legumes, alcohol and NSAIDs. The following foods should be eliminated for 4-12 weeks:

  • Gluten

  • Dairy

  • Soy

  • Eggs

  • All Grains

  • Beans and legumes, such as peanuts

  • Corn

  • Nuts

  • Seeds (including seed-based spices like coriander and cumin, and seed based oils)

  • Nightshade vegetables (including potatoes, tomatoes, bell peppers, hot peppers, eggplant, potatoes, and spices derived from them like paprika, cayenne, and curry)

  • Preservatives, emulsifiers and thickeners such as careengeen, ascorbic acid, citric acid, sodium benzoate, calcium propionate, BHA and BHT

  • Refined oils, such as canola oil and vegetable oil

  • Sugar and artifical sweeteners

  • Coffee

  • Chocolate

  • Alternative sweeteners, such as stevia, erythritol, xylitol, and mannitol

  • Alcohol

  • NSAIDs

The temporary elimination allows time for the body to calm autoimmune attacks, reduce inflammation, promote gut healing and diminish autoimmune-related symptoms. After the elimination phase, you get to reintroduce foods. There are various different methods for reintroduction, but in general, you will reintroduce foods slowly and one at a time. Some people can reintroduce foods after 4-5 weeks whereas others require a longer time to heal. 

emily morrow autoimmune protocol

Foods to Include on AIP

Equally as important as eliminating and removing trigger foods, is nourishing the body with nutrient density-- whole food substances that regulate the immune system, repair damaged tissues and support the normal functioning of each body system. The following foods are allowed and should be enjoyed while on the Autoimmune Paleo Protocol:

  • Pastured, grass-fed, organic meat (beef, chicken, turkey, lamb, pork and wild game) available at Thrive Market and Vital Choice

  • Grass-fed and pasture raised bone broth and organ meats (available at Thrive Market and Vital Choice)

  • Wild-caught fish and shellfish (available at Thrive Market and Vital Choice)

  • Grass-Fed Collagen and Gelatin Protein

  • Animal fats like tallow, lard, and duck fat from pastured animals

  • Coconut oil and red palm oil from sustainable sources

  • Healthy fats such as avocados, olive oil and avocado oil

  • Moderate fruit (limit to 15 grams of fructose per day)

  • Organic Vegetables (minus nightshades) such as cruciferous vegetables, sweet potatoes, roots and tubers

  • Sea Vegetables (excluding algae like chlorella and spirulina which are immune stimulators)

  • Low glycemic fruits, limit 2-3 servings per day or 15-20 grams fructose per day

  • Herbs and spices that are not seeds or nightshades, like basil, thyme, rosemary, turmeric, and garlic

  • Coconut products, such as coconut flakes, coconut shreds and coconut butter

  • Vinegars, such as coconut vinegar, apple cider vinegar and balsamic vinegar

  • Fermented foods like sauerkraut, kombucha and coconut or water kefir

  • Matcha, green tea and herbal teas

  • Sea salt and Himalayan pink salt

  • Occasional use of honey or maple syrup (limit to 1 tsp per day)

For more information, check out this AIP foods list as well as the grocery list provided by Phoenix Helix.


Lifestyle Goals of AIP

Diet is only one component of healing on AIP. It is equally as important to balance other areas of your life as well. Reducing and managing stress, prioritizing sleep, daily exercise/activity and limiting inflammation are key.

The Primary Lifestyle Goals of AIP:

  • Get at least 8 hours of sleep per night

  • Do not eat on the run; make time for your meal and really chew your food

  • Limit stress and practice meditation or yoga

  • Participate in daily activity, preferably with sunlight exposer

  • Avoid sitting too long; set a timer for every hour to get up and move around or do a few squats or jumping jacks

  • Create an emotional support network with family and friends

  • Schedule time for socialization

  • Drink plenty of filtered water


My Experience with AIP

After blood work revealed the following: deficiencies in Vitamins B6, B9 and B12, overworked kidneys, elevated liver enzymes and interferences with liver and estrogen detox and low white blood cells, I opted to follow the Autoimmune Paleo Protocol.

Suggested supplements to facilitate healing and detox while on AIP:

  • Methyl Care for blood vessel health and regulation of homocysteine metabolism

  • Ultra Clear Renew for metabolic detoxification, alkalization and heavy metal metabolism

  • L-glutamine powder to support immune function and gut healing (see supplements page)

  • Magnesium to support sleep and over 300 enzymatic and physiological functions (see supplements page)

  • To boost immune function: Omega 3 Fish Oil, Vitamin D3 and Zinc (all from Thorne Research); contact me to set up your account

After 30 days of the AIP protocol, I noticed significant improvements to my overall health and wellbeing. Most notable reactions after 1 month:

  • Reduced sugar and salt cravings

  • Improved sleep, feel rested when I wake up

  • Less bloating/cramping

  • Reduction in water retention

  • Decrease in facial and eye puffiness

  • Improved mental clarity

  • Minimal headaches/ no migraines (something I have always struggled with)

  • Increased ability to manage stress

  • Less joint pain

  • Improved energy


Is AIP for Me?

If you suffer from an autoimmune disease or are experiencing some of the autoimmunity symptoms listed above, AIP might be worth a shot. Always consult your doctor before changing your diet and lifestyle. The AIP protocol can positively impact your gut and help you learn more about your body due to the fact that it prioritizes anti-inflammatory foods and nutrient density, and helps you identify foods that trigger unpleasant symptoms or flare-ups.

A lot of people can improve their health simply by following a paleo diet. Jessica from the AIP lifestyle encourages people to read  When AIP Is A Crutch Not A Cure before starting the AIP protocol.

To get started, check out the AIP Survival Guide, an amazing resource!






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