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Autoimmune Protocol AIP Reintroduction Phase

Autoimmune Protocol AIP Reintroduction Phase

Autoimmune Protocol AIP Reintroduction Phase

The autoimmune protocol (AIP) is a nutrition and lifestyle protocol specifically designed to help those with autoimmune disease find relief from their symptoms.  

The nutrition side of the AIP includes the elimination phase, the reintroduction phase, and the maintenance phase.  You can learn more about the elimination phase here.  You can download a free AIP foods list here

This article and video will help you understand the ins and outs of the autoimmune protocol AIP reintroduction phase, the importance of reintroducing foods, and how to tell when a reintroduction fails.  


When to Start to Reintroduce Foods on the AIP Diet

There are no set timelines for when to reintroduce foods.  Keep in mind the importance of bio-individuality, meaning what works best for one person will look differently than what works best for another person.  

One person may start reintroductions after just 30 days on the AIP elimination phase, while another person may wait a number of months to start reintroductions.

In an ideal situation, you’d want to wait until you feel relief from your autoimmune symptoms before you reintroduce foods.

However, if you are seeing some improvements in your health and feel ready to reintroduce some foods, you can start to try some reintroductions after 4 weeks.  However, try not to let cravings determine your reintroduction choices.

If you are not seeing improvements on the AIP elimination phase after 3 months, I recommend working with a functional medical doctor or a nutritional therapy practitioner with AIP experience to help you personalize the AIP as well as troubleshoot.

Some Things to Consider Before Reintroducing Foods

When not to reintroduce foods…

There are times when it is not recommended to reintroduce new foods since it may be hard to identify the cause of a reaction. These times include: fighting an infection, lack of sleep, increase in stress, or after a strenuous workout.

What is your motivation?

If your motivation for wanting to move into the reintroduction phase stems from cravings, I recommend holding off. Instead, work through your cravings and emotional eating tendencies. Taking the time to overcome cravings and allowing your taste buds to change can set you up for long term success.

Still experiencing symptoms?

If you are still experiencing symptoms on the elimination phase, your immune system is most likely still attacking your organs and body. Take the time to troubleshoot either independently or with a functional medical doctor or nutritional therapy practitioner experienced with the autoimmune protocol and autoimmunity.

Personalizing your journey…

Remember that during this process you are learning more about your body, what foods help you feel your best, and how to live well with your autoimmune disease. Your journey will not look like anyone else’s journey.

When you reintroduce a certain food is your choice, but keep in mind some reintroduced foods will be “sometimes” foods, and some you may not reintroduce at all.

Why is it important to Reintroduce Foods?

After finally finding relief from autoimmune symptoms during the elimination phase of the autoimmune protocol, it can be tempting to stay on the elimination phase.

Nutrient Density

There are many nutrient dense foods eliminated initially on the AIP that provide your body with additional needed nutrients. Examples include nuts, seeds, eggs, grass fed dairy, and more.

Increase in Variety

Reintroducing foods allows you to increase the variety of nutrient dense foods you eat. Not only is this great for consuming a variety of nutrients, but it will also help you avoid getting bored!

Easier to Travel & Eat Out

As you reintroduce foods, you will have more options when eating out and traveling.


Going through the reintroduction process will give you valuable feedback about your body.

Even if you fail a reintroduction initially, that provides you with feedback about your body.

What About Fear Surrounding Reintroducing Foods?

Please keep in mind that it can be a normal part of the process to feel fear when it comes to reintroducing foods.

For many of us, we find relief from our autoimmune symptoms for the first time in years during the elimination phase of the autoimmune protocol.

So we naturally may not want to reintroduce foods for fear of triggering our autoimmune symptoms again.

Be mindful of your fear, and take steps to work through it. Practice extra self care, and be mindful of stress. The increase in stress may actually be the culprit triggering your symptoms, rather than the reintroduced food.

Take your reintroduction phase as slowly as you need to, in order to work through your fears and stress.  Seek professional help if needed and if your fear is stopping you from progressing through the AIP reintroduction phase.

How to Reintroduce Foods

  • Choose a food to reintroduce, then plan to eat it two or three times in one day (then you will avoid it completely for a few days).
  • When you eat the food for the first time, eat just half a teaspoon or even less, then wait for fifteen minutes.
  • If you experience any symptoms (see below for symptoms to look for), do not eat any more of the food. If you do not experience any symptoms, eat a small bite of the food (about one teaspoon), then wait fifteen minutes.
  • If you experience any symptoms, do not eat any more of the food. If you do not experience any symptoms, eat a slightly bigger bite of the food (about one and a half teaspoons), then wait two to three hours and watch for symptoms.
  • If you still do not experience any symptoms, eat a normal-sized portion of the food.  Plan on not eating that food again for 5 to 7 days.
  • Watch for symptoms in the days that follow.
  • Plan on not reintroducing any other foods during the 5-7 days.
  • If you have no symptoms at all during the process or in the days that follow, you can consider the reintroduction successful and reincorporate this food into your diet!
  • Note:  just because you may not tolerate a reintroduced food well now does not mean you will not in the future (exceptions include foods that you are allergic to).

What Symptoms to Watch For

Symptoms of a reaction aren’t always obvious, so keep an eye out for any the following:

  • Symptoms of any diagnosed disease returning or worsening
  • Gastrointestinal symptoms: tummy ache, heartburn, nausea, constipation, diarrhea, change in frequency of bowel movements, gas, bloating, undigested or partly digested food particles in stool
  • Reduced energy, fatigue, or energy dips in the afternoon, or a second wind in the late evening that makes it hard to go to sleep at a good time
  • Cravings for sugar, fat, salt, or caffeine
  • Pica (craving minerals from nonfood items like clay, chalk, dirt, or sand)
  • Trouble falling asleep or staying asleep, or just not feeling well rested in the morning
  • Headaches (mild to migraine)
  • Dizziness or lightheadedness
  • Increased mucus production: phlegm, runny nose, or postnasal drip
  • Coughing or increased need to clear your throat
  • Itchy eyes or mouth
  • Sneezing
  • Aches and pains: muscle, joint, tendon, or ligament
  • Changes in skin: rashes, acne, dry skin, little pink bumps or spots, dry hair or nails
  • Mood issues: mood swings, feeling low or depressed
  • Feeling anxious, less able to handle stress

Source:  Reintroducing Foods After Following the Autoimmune Protocol by Dr. Sarah Ballantyne

Recommended Order of Reintroductions

There are options when it comes to deciding which foods to reintroduce first.

You can either start to reintroduce the foods you miss most, or you can start by reintroducing the foods least likely to cause a reaction.

Dr. Sarah Ballantyne, author of The Paleo Approach and The Autoimmune Protocol ebook, offers a suggested order of food reintroductions that takes into account the likelihood of reaction as well as the nutritional value of the food.

Included in the first stage are foods that are most likely to be well tolerated when reintroduced, while the fourth stage includes foods that are the least likely to be well tolerated, and you may not wish to challenge depending on your situation.

It is recommended to try to reintroduce the foods in stage 1 that you want to reincorporate (except any that you are allergic to or have a history of severe reactions to) before proceeding to stage 2, and so on.  

Please note even if you have a reaction to food in the first stage, you can still move on to challenging / reintroducing foods in the second stage and so on.  

With that said, if you find you are not able to tolerate most or all of the foods in the first stage, you may want to stop reintroductions for a few weeks or so before trying them again.

In the meantime, continue working on your wellness journey and improving gut health.  If you are not already doing so, consider working with a functional medical doctor or nutritional therapy practitioner who can help you with gut healing as well as recommend any personalized supplement needs for digestion.  

A Note on Oral Intolerance

One of the questions I sometimes get is something like “why am I having a reaction to a non AIP food that I used to eat all the time when I never noticed a reaction before?”
Eileen is a friend of mine, and she does a wonderful job of interviewing Dr Datis Kharrazian about the ins and outs of oral intolerance, and what we can do to improve our tolerance as autoimmune patients. Dr. Datis is one of my favorite autoimmune experts!
Listen all the way to the end and you will pick up some great nuggets of information and tips. At 36:00 is when Dr. Datis specifically addresses if AIP can cause oral intolerance (increased sensitivity to more foods).
I hope you enjoy! I love to listen to podcasts when I’m out walking or cooking in the kitchen, and Eileen’s is one of my favorites.

Does the 80/20 Rule Work for the Reintroduction Phase?

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.

AIP reintroduction phase is not an 80/20 rule kind of eating plan.  It is an important follow up to the temporary healing protocol / elimination phase of the AIP.

The goal of the reintroduction phase is to add in previously eliminated foods to see if the food triggers your immune system.  If you switch to the 80/20 rule, it will be hard to tell which foods are triggering your symptoms and which reintroduced foods you tolerate well.

Please Know

It is normal to feel some fear and apprehension about the reintroduction phase of the autoimmune protocol. It is possible to work through the fear and progress in your AIP journey.

Your AIP journey is uniquely your own. It will not look like anyone else’s…and I think that is a beautiful thing.

Remember that symptoms are feedback from our body. If a reintroduction triggers symptoms, it is not a failure. It is valuable feedback from your body, and it does not mean you will never be able to reintroduce that food again. It simply means not right now.

Remember to allow yourself to feel all the feels, but to also cultivate a growth mindset, positivity, celebrate how far you’ve come, and to practice lots of self care.


DISCLAIMER: Links I post may contain affiliate links. If you purchase a product or service with the links that I provide, I may receive a small commission at no additional charge to you.  Thank you for supporting my work and my website so I can continue to provide you with free content each week!

Comments (2)

Hi Shannon, Foods I don’t see in any of the reintroduction phases means it’s best to not reintroduce those? I’m thinking about other types of beans (black, cannellini) and whole grains like whole wheat products. Thanks, Pam

Shanna Nemrow

Hi Pam! The type of beans you mentioned are included in stage 4 reintroductions – under “traditionally prepared or fermented legumes.” As far as whole grains containing gluten, many choose not to reintroduce gluten for a number of reasons, including the effect of gluten on the gut. If you decide to reintroduce gluten containing products, that would be after stage 4 if you are going in order of the recommended reintroductions. Wishing you all the best! Hugs, Shanna

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