Reintroduction: Phase 3 of the Autoimmune Protocol

Below is the full transcript of Episode 54 of the Autoimmune Wellness Podcast.
This transcript is provided for accessibility and reference.

Title: Reintroduction: Phase 3 of the Autoimmune Protocol | Deep Dive (Ep 054)

Reintroduction: Phase 3 of the Autoimmune Protocol (Ep 054)

[00:00:00] Introduction: AIP Reintroduction Phase History and Updates

Reintroduction. It’s the most misunderstood, but also the most powerful part of The Autoimmune Protocol. So everybody loves to talk about elimination, but reintroductions is where the real magic happens. Because this phase is not just about adding foods back, it’s a methodical process of self-discovery.

You might be surprised to hear that for many people on AIP, the Reintroduction Phase is the longest and most challenging part. It’s also where a lot of people learn exactly what their bodies need to thrive and how to make eating for autoimmune health long-term truly sustainable.

And here’s something else to know right up front. There have been major updates to The Autoimmune Protocol that change how reintroductions are approached today. So, a lot of what’s floating around online is now outdated or incomplete.

If you’ve tried to navigate the Reintroduction Phase of AIP before, or if you’re about to start, you’re going to want to hear what is brand new. Today I’m going to break down everything you need to know about the Reintroduction Phase, how to know when you’re ready, how to reintroduce food safely, which order to reintroduce specific foods, and how to interpret your body’s feedback so that you can build a diet that supports you for the rest of your life.

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Welcome back to the Autoimmune Wellness Podcast. I’m Mickey Trescott, and this is part four of my AIP Deep Dive series. If you’ve been following along, we started with a broad overview of The Autoimmune Protocol, what it is, how it works, why it’s such a powerful tool for managing autoimmune disease.

Next, we explored the first and second phases of the protocol, the Transition and the Elimination Phase. We talked about how to track your baseline, how to prepare, and then what specifically to eat, what to avoid, and how to make this all sustainable in real life.

And today we’ve made it to the third phase of AIP. This is the Reintroduction Phase, and like I said before, this is where all of the hard work during transition and elimination really pays off because while elimination helps calm inflammation, reintroduction helps you build a personalized diet that supports your best health.

So just a quick reminder before we begin. What I share here is for education and inspiration only, it’s not medical advice. So make sure to make any health decisions in partnership with your healthcare team.

[00:02:34] What the Reintroduction Phase Is—And Why It Matters

So let’s start with what this phase actually is. Reintroduction is the systematic process of bringing previously-eliminated foods back into your diet to test for tolerance.

This approach is supported by decades of scientific research in elimination diet, food allergy and food sensitivity studies. And it’s still considered the gold standard for determining food sensitivities. And yes, this is even compared to blood tests, which I will discuss in a further episode.

Reintroduction has two main goals. First, you’re looking to identify which foods are well tolerated so that you can confidently expand your diet. And second, to pinpoint which foods still cause reactions so that you can continue supporting your body’s healing process.

So here is what’s really important to understand. The Elimination Phase of AIP is never meant to be permanent. In the early days of The Autoimmune Protocol, before we had structured guidance, many people made the mistake of staying in elimination too long and some indefinitely.

Some people were afraid to reintroduce foods while others just didn’t know when or how to start. Raising my hand because I was definitely one of these people. But we now know that remaining in elimination long-term isn’t a part of the plan and it can actually work against you. Staying there too long can create nutrient gaps, making eating socially and emotionally stressful, and it can even lead to food fears. That’s why a clear reintroduction process is essential to working through AIP.

This is the step that transforms the protocol from a restrictive diet to one that is flexible and personalized to your lifestyle. And again, this is where AIP becomes uniquely yours. It yields a way of eating that is nourishing, sustainable, and just for you.

[00:04:27] When to Begin the Reintroduction Phase

So when are you ready to start reintroductions? This is one of the most common questions I get about The Autoimmune Protocol, and the answer might surprise you. Most people are ready to begin reintroductions after about 30 to 90 days in the Elimination Phase, once they’ve experienced measurable improvement from their baseline symptoms. We discussed this in the last episode.

This is the timeframe that gives your body enough space to calm inflammation, repair the gut lining and restore immune balance, setting the stage to accurately test how it responds to individual foods.

But let’s unpack what measurable improvement really means, because it absolutely does not mean perfection. And this is a trap that I fell into when I did my original AIP. You don’t need to feel completely healed or symptom free to begin. The goal isn’t total recovery. It’s just enough progress to see how foods are affecting you.

For example, maybe your energy levels used to crash by mid-afternoon, and now you’re making it through the day without needing a nap. Maybe your skin is clearer, or your joint pain is less frequent, or your digestion feels more consistent. Even small, steady improvements like sleeping through the night, or having fewer headaches count as meaningful signs of healing as long as you can track them.

This is where that tracking practice that you learned about starting in the Transition Phase, but then you’re using through the Elimination Phase, really pays off. So in that Transition Phase, you took time to establish your baseline. This was the clear picture of how you were feeling before you started AIP.

Maybe you noted things like your energy levels through the day, your digestive symptoms, your sleep quality, your moods, skin changes, or how often you were experiencing flares of your specific condition. That baseline is your before snapshot. It helps you see exactly where you started.

Then during the Elimination Phase your tracking shifted into capturing trends over time. You might have noticed that certain symptoms started to lessen. Your sleep became more consistent. You were waking up with steadier energy. Now, as you prepare for reintroduction, those notes become one of your most valuable tools. So I want you to pull out your symptom journal or your app and just take a look at how things have changed.

Are your symptoms just as frequent or as intense as before? Or have they eased up even a little bit? For example, maybe your fatigue was an 8 when you started and now it’s closer to a 4. Maybe your digestion used to fluctuate daily, but now you have regularity and comfort. These shifts matter, even if they don’t feel dramatic.

When you can look at your own notes and say, things aren’t perfect, but they’re definitely improving, that is your clue that your body is ready for the next step. And here’s why this matters so much. If you start reintroducing foods before you’ve seen a measurable improvement, you’re not going to get clear results.

The inflammation and immune reactivity from before elimination can mask your body’s true responses to foods. It can make everything feel like a trigger or worse, it can be impossible to tell what is actually causing your symptoms. So reintroducing without this progress is like trying to test food sensitivities while your immune system is still in overdrive. You’re just not going to get accurate feedback.

Now, on the other side of that, if you’ve been in elimination for more than 90 days and you haven’t seen any meaningful improvement, that is not a reason to double down and get stricter. It’s actually a sign to take a pause, and enter troubleshooting. Working with an AIP Certified Coach or a healthcare provider can help you figure out what is holding you back, whether that is an underlying infection, maybe nutrient deficiency, hormone imbalance, or something else that diet alone can’t fully address.

You’re not waiting for perfection, you are looking for progress. Once you can see and feel that consistent improvement, even if it’s partial, you have earned the green light to begin the next phase.

[00:08:34] Food Reintroduction Procedure

Now that you’ve confirmed you’re ready to start, let’s walk through exactly how to reintroduce foods safely and effectively. The good news is that the reintroduction procedure has been updated, and it’s the same whether you’ve followed Core AIP, or Modified AIP. These updated steps are based on what’s worked best across thousands who have used AIP, and they’re designed to help you get clear, reliable results.

Here’s how the process works. First, you’re going to choose one food to test from the reintroduction stages chart from your elimination plan, and only that food. Avoid trying anything else new that day so that you can clearly identify your body’s response.

Then you’re going to start small. You’re going to begin with about half a teaspoon, maybe a little more of that food. You are going to eat it and you’re going to wait for 15 minutes. Now if you notice any kind of reaction, so anything from digestive discomfort to itching, fatigue, or mood changes, stop the test and note it in your journal. That food is not ready for reintroduction yet.

If you don’t have a reaction, increase to about one teaspoon, wait another 15 minutes. If you’re still doing fine, you’re going to try a little bit more and observe for two to three hours.

So if you continue to feel well, go ahead and have a normal portion of that food. And after that normal portion, you’re going to wait three to seven days before reintroducing the next food. During that waiting period, watch for delayed symptoms or changes, which these are actually very common, so I want you to pay attention here. There are things like shifts in digestion, in joint pain, in sleep, quality energy, skin clarity or mood.

And that spacing is essential. It really gives your body enough time to show any delayed reactions and ensures that you can confidently connect a symptom or even a lack of one to a specific food.

And do not forget to track everything, whether you’re using a notebook or an app or a spreadsheet. Note the food that you tested, how much you ate, or any changes that you notice in the days that follow. These details help you build a clear picture of what’s working and what is not, and what’s worth retesting later.

Now, I just want to make a note here that if there is a food that you have a known allergy or extreme sensitivity to, you absolutely do not want to engage in this process with that food, and you always want to follow the guidance of your medical practitioner in how to proceed with that.

Throughout the reintroduction process, you’re not just adding foods back, you’re learning how your body communicates and tells you when something is working or not working for you. The more intentional you are with this process, the more confidence you’ll have in building your long-term, personalized version of AIP.

If you’d like a little help keeping track, I’ve created a food reaction checklist that gives you space to record your notes and observations. You can download it for free as part of the AIP Foundation Series theautoimmuneprotocol.com/foundations.

Next we’ll talk about how to decide the order of food reintroductions. Now remember that with the new update to The Autoimmune Protocol, there are now two distinct paths you might be following. Core AIP or Modified AIP. Both are designed to help you discover your personal food tolerances, but they differ slightly in which foods are eliminated.

It doesn’t matter which version you’re following, when it comes to the reintroduction procedure, that is going to be the same structured, evidence-based approach to testing foods one by one. Now the difference is going to be in which foods you’re starting with. Since some of the foods that were already included in Modified AIP might fall into earlier stages for those coming from Core AIP.

So with that context in mind, let’s walk through the stages of reintroduction for both Core and Modified AIP. These stages are organized intentionally. They include the most nutrient-dense and least likely to cause a reaction foods to the ones that are more commonly problematic. These early foods you’ll test tend to be packed with vitamins, minerals, and healthy fats. These are nutrients that actively support your healing process.

So these first reintroductions often bring easy wins. They’re also the most likely to be well tolerated, helping you gain confidence and momentum as you expand your diet. Now, as you progress through the stages, the foods become more complex and more likely to trigger a response.

When you approach reintroductions in this structured step-by-step way, you’re not just adding foods back, you’re building a foundation for a diverse, flexible, and sustainable way of eating that is personalized just to you.

[00:13:18] Core AIP Food Reintroduction Stages

Let’s start with the reintroduction stages for Core AIP, which are divided into four levels. Each stage moves from the foods that are most nutrient dense and the least likely to cause a reaction to those that are more likely to trigger symptoms.

For Core AIP, stage one, the lowest-risk, most nutrient-dense foods are egg yolks, legumes with edible pods, these are going to be things like green beans, peas, snow peas, and sugar snap peas. Seed based spices, so celery seed, coriander, cumin, fennel, et cetera. Nut and seed oils, but not the nuts themselves, chocolate and coffee and ghee. And ghee is clarified butter with virtually no milk proteins.

For Core AIP stage two, we call these the moderate-risk foods. At this stage, these foods are still really nutrient-dense, but some people find that they have sensitivities to them. Whole eggs, this is going to include chicken, duck or quail, any species including the whites.

Tree nuts and seeds in whole or butter form. And yes, you do need to reintroduce each one on their own because people often have sensitivities to one or a few and not others. So this includes things like almonds, pecans, sunflower seeds, pumpkin seeds, and others. Dairy fats, so now we’ve moved on from ghee to butter and oil. And then lastly, alcohol in small amounts, gluten-free.

Then we move on to the Core AIP stage three foods, which are higher-risk. So these are more likely to cause inflammation or immune activation in specific people, so make sure to reintroduce them mindfully and always one at a time.

Nightshades, so this includes bell peppers, peeled white potatoes, eggplant, and paprika. And yes, the peels do cause some people problems. So when we reintroduce nightshades, we like to start with these foods and then you can progress on if you tolerate them.

Full-fat dairy. So we’ve moved on from butter to milk, cheese, yogurt, kefir, sour cream, and whey protein. Legumes. This is where we get to reintroduce the rest of the legume family. So chickpeas, lentils, split peas are the examples there of the most easy to tolerate legumes.

And then moving on to Core AIP highest-risk foods. So these are the foods that are most likely to cause symptoms or trigger inflammation. So I like to be extra cautious with this final category.

For nightshades it includes chili peppers, cayenne, tomatoes, goji berries, and ashwagandha. A note here that some people find that they have really varying sensitivity to the nightshade family, specifically. You’re going to want to test these things one at a time to find out what works and what might not work for you.

Gluten-free grains and pseudo-grains. This is going to be where you get to reintroduce rice, oats, millet, buckwheat, quinoa, amaranth, and teff. And then legumes, black beans, kidney beans, peanuts, soy, and others, alcohol in larger amounts, if that’s something that you decide to partake in.

By following these stages, you’ll move from those easy wins to maybe some of the more complex foods that are harder for some people to reintroduce, giving your body time to communicate before you add in the next category.

[00:16:46] Modified AIP Food Reintroduction Stages

Now if you followed Modified AIP your reintroduction process will look a little different. Because Modified AIP begins with a more flexible Elimination Phase. You’ve already been eating some of the foods that would appear in the early stages of Core AIP.

That means you’re starting further along in the process and your reintroductions will be divided into just two stages instead of four. The same rules apply. Introduce one food at a time, follow the reintroduction procedure carefully and allow a few days between tests to track your results.

Here’s how the stages break down for Modified AIP. Modified AIP stage one, again, lowest-risk, most nutrient-dense foods, these foods are the best place to start. In stage one, we start with egg yolks, not the whites, very similar to Core AIP. You can use any species of egg, but you’re just going to be having the yolks first.

Next we move on to nuts. So these are all different types of nuts, almonds, Brazil nuts, chestnut, hazelnut, macadamia, nuts, the list goes on. Just make sure that you are tracking them one at a time for the same reason that I mentioned before.

With dairy, since we’re already including ghee in Modified AIP, we’re going to start with butter, buttermilk, cheese, cottage cheese, cream cheese, milk curds, dairy, protein isolates, heavy cream, kefir, sour cream, ice cream, whey, whey protein isolate, whipping cream, or yogurt. Now that’s a long list of dairy. I recommend going and testing each dairy product individually because like other food families like nightshades, people tend to have varying ranges of tolerance.

And then next, speaking of which, we have nightshades, which is limited to just paprika and peeled potatoes.

Now, once you have completed stage one for Modified AIP, we move on to stage two, which has the remainder of the foods. That includes the whole egg or the egg whites , gluten-free cereal grains, so these are corn and millet, and oats, sorghum, et cetera. We’ve got the rest of the nightshade family vegetables and spices, so bell peppers, cayenne , eggplant, goji, berries, et cetera. And then also the last thing is alcohol, in smaller quantities, if that is something that you choose to include.

Now if you’d like to see the reintroduction stage charts for both Core and Modified AIP laid out visually, I’ve created a downloadable chart that makes it easy to follow along as you work through your reintroduction process. You can grab it for free at theautoimmuneprotocol.com/foundations.

[00:19:29] Tracking and Interpreting Food Reintroduction Results

So now that you know the procedure for reintroductions and how to determine the order of foods, let’s talk about tracking one more time.

Just because this is how you are going to determine which foods truly work for you. By this point, you already know how powerful tracking can be, and during reintroduction it becomes absolutely essential. This is where that symptom tracker really earns its keep because it’s going to be your main tool for connecting what you eat with how you feel, and identifying whether any new symptoms are related to a specific food.

So after testing each new food, make sure that you record the date of the food tested to keep your reintroductions organized and easy to follow. The amount that you ate, note each stage, any immediate reactions, these are going to be things that appear within 15 minutes to a few hours, and then any delayed reactions. Anything that shows up over the next one to three or even up to seven days if you’re waiting that long. And I will tell you that there have been a lot of studies out on delayed reactions, so don’t be afraid to look for connections in that four to seven day range because they absolutely are happening.

Common signs of food sensitivities can include digestive upset, skin rashes, joint or muscle pain, headaches, brain fog, anxiety, mood swings, but also pay attention to subtle changes, things like restless sleep, lower motivation, or the return of symptoms that you had previously.

That’s actually one of the easiest way to tell that a food wasn’t working for you specifically. Say you had a rash that went away during the Elimination Phase, and then it comes back when you start reintroducing a food, it’s pretty easy to make that connection. Now if you experience a negative reaction, you want to remove that food again and wait at least two weeks before considering a retry.

Now that two weeks is just a suggestion. Sometimes you feel really good after a few days, so you can modify that if it works for you. But you really want to give your body time to settle and return to your baseline before testing another food. You do not need to go back all the way to the Elimination Phase, you just need to go back to before you reintroduced the specific food that caused the reaction.

So If you reintroduce a food and you feel fine, no symptoms, no discomfort, and your energy levels are steady, that’s a successful reaction. Guess what? Celebrate that win, make a clear note in your tracker and move on to your next test when you feel ready.

Now, the goal here is not speed. You do not want to move too quickly through reintroductions. Every food you test gives you a valuable insight into what supports your body best, helping you create a version of eating that’s not just for a healing process, but sustainable for the rest of your life.

[00:22:21] Identifying and Navigating “Gray Area Foods”

Now before we close, I wanted to discuss “gray area” foods because it’s something that comes up for almost everyone who goes through reintroductions. “Gray area” foods are what I call those that don’t fall neatly into those “yes” or “no” categories.

You might find that you don’t have a bad reaction to them, but they’re not completely tolerated either. For me, “gray area” foods are reacted to sometimes, but not always. And often the reaction will depend on maybe how much you eat or what other foods you’ve had alongside them, maybe your stress levels that day.

For me, eggs were a “gray area” of food for a long time. At first, I couldn’t tolerate them at all. Then after I had progressed through some deeper healing, I could eat them occasionally, say some scrambled eggs on a weekend brunch or on vacation. I would feel mostly fine, but if I started eating them every day, my symptoms would start to creep back in. And so that’s the point. The “gray area” of foods remind us that tolerance isn’t all or nothing. As much as we want to put foods in these neat categories of “yes” and “no”, it’s really a spectrum that can shift with time, stress, or even hormone changes.

So if you suspect that you found a “gray area” food, the best approach is to reintroduce it slowly and occasionally. Give yourself time to observe how your body responds over multiple exposures. If you get a reaction that is mild and predictable, you might decide that food is worth including sometimes like while you’re on vacation, maybe at a special occasion, or when it simply brings you a lot of joy.

On the other hand, if you find that it consistently leads to discomfort or inflammation, that’s also valuable information. You can pull it back out and try it again later. So the goal of AIP is never about perfection. You guys have heard me talk about this a lot. It’s just about awareness. “Gray area” foods give you a chance to practice that awareness and build flexibility into your personal AIP template.

Over time, you’ll learn which foods nourish you daily, which you enjoy occasionally, and which ones are better left off your plate for good.

[00:24:27] Types of Reactions to Expect When Reintroducing Foods

Let’s talk a little bit more about what types of reactions you might actually notice during reintroductions. Reactions can look different for everyone, and they aren’t always dramatic or immediate. Some people expect a major flare up right away, but most of the time reactions are really subtle. They’re little shifts that are easy to miss if you’re not paying attention. That’s why tracking and observation are so important.

I want you guys to be on the lookout for two different types of reactions, immediate and delayed. Immediate reactions happen within the first few minutes to about three hours after eating a food. These are the easiest to spot and might include digestive symptoms like bloating, nausea, cramping, reflux, skin changes like flushing, itching or hives, respiratory or sinus changes, this happens to me , sudden congestion, sneezing, or a scratchy throat, quick shifts in energy or mood, feeling wired, anxious, or maybe unusually tired right after you eat.

And we’re all looking for these quick reactions. We all want to eat a food and then be, aha, that’s what it was, but it’s not always that easy.

Now, delayed reactions can take up to three to seven days to show up, and they’re often the ones that sneak by if you’re not tracking carefully. They include things like increased joint or muscle pain, headaches or migraines, fatigue that feels out of proportion to your activity level or activities, mood changes like irritability or brain fog, digestive disruptions that appear in a delayed effect, so things like constipation, loose stools, or even changes in appetite, poor sleep or waking up feeling unrested.

You might notice one symptom or several symptoms kind of working together. And sometimes the pattern only becomes obvious after testing a food multiple times. That’s where taking this into practice and being gentle with yourself, not trying to learn everything in a very short period of time is essential.

And remember, reactions don’t always mean that a food is bad or off limits forever. Sometimes it just means that for right now your body isn’t ready for it. You can always pause, give yourself more time and come back to the food later.

To make all of this easier, I’ve created a Food Reaction Checklist that walks you through what to look for and gives you the space to document your responses while reintroducing foods. You can download it for free as part of the AIP Foundation Series at theautoimmuneprotocol.com/foundations.

Having a checklist handy makes it that much easier to stay organized, spot patterns, and understand your body’s messages with confidence.

[00:27:12] Life After Reintroductions—Your Personalized Template

So what happens after the Reintroduction Phase? This is where your hard work truly pays off. You have spent all of this time eliminating, observing, methodically reintroducing foods, and now you have something incredibly powerful.

Personal data. You know which foods your body handles extremely well, which ones it needs more time with, and which ones are better off completely left off your plate. Through this, you have built your personalized AIP template, a long-term way of eating that reflects everything you have learned about your body.

Your template may look very different from someone else’s. Even if you share the same diagnosis or symptoms. You might be able to enjoy eggs or small amounts of dairy while someone else can’t. You might find that certain nightshades or legumes work fine for you while others remain off the table for now.

What matters most is that it supports your body, your lifestyle, and your goals. And here’s the thing, your template is going to continue to evolve. Mine absolutely has in the 15 years I’ve been doing this. Healing is not static. What doesn’t work for you today might actually be totally fine a year from now, and that’s completely normal.

Some people find it helpful to return to a little more of an elimination-style diet periodically. Now, I don’t want to say this is like a reset or doing it again, but if you go through a flare, maybe you’re recovering from travel, or maybe when life stress piles up, you know the foods to remove that are going to give you a pretty good bang for your buck in recovering there to reset inflammation and rebuild awareness.

On the flip side. Others like to maintain their personalized vision indefinitely and adjusting gently as they go. No way is right or wrong.

Most importantly, remember this, you’re not “done” with AIP. You are actually now integrating it. So all of the lessons that you learn through this process, how to listen to your body, how to respond, how to nourish yourself deeply, all of these become tools that you will learn for the rest of your life in managing your health with autoimmune conditions. You now have the awareness to make empowered choices, whether that is choosing a food that you know might cause a mild reaction on a special occasion or saying no because it’s just not worth the trade off, and that’s what real food freedom looks like.

[00:29:36] Wrap Up and AIP Foundations Series

If today’s episode gave you confidence about bringing foods back, be sure to subscribe so you don’t miss the next Deep Dive episode. We’re going to talk about nutrient density and deep healing and how it is so much more than just what we are eating or not while we go through AIP.

And if you’d like printable reintroduction charts for both Core and Modified AIP as well as that symptoms checklist. Go ahead and download them for free inside my AIP Foundation Series at theautoimmuneprotocol.com slash foundations. Thanks so much for listening, and I’ll see you next time.