The AIP Transition Phase Explained: How to Prepare for Success Before Elimination

Below is the full transcript of Episode 52 of the Autoimmune Wellness Podcast.
This transcript is provided for accessibility and reference.

Title: Transition: Phase 1 of the Autoimmune Protocol | Deep Dive (Ep 52)

[00:00:00] Introduction: History of the AIP Transition Phase

In the early days of The Autoimmune Protocol, there was no such thing as a Transition Phase. You just jumped right in and started eliminating foods, and honestly, it was overwhelming. Many people gave up, not because they lacked motivation, but because it was simply too much, too fast.

In those early days, many people, myself included, were clearing out our pantries overnight, shifting to all new recipes and cooking, all while managing flares of our autoimmune conditions and trying to keep up with everyday life.

Even the most determined found it hard to sustain, and it was really common for people to go through these cycles of starting and stopping the Elimination Phase of AIP.

Later, a phased approach became popular, removing food groups one at a time. That helped those who needed a gentler dietary transition, but it didn’t address the deeper challenges that so many people faced— how do you prepare mentally, logistically, and emotionally for such a major lifestyle change like the Elimination Phase?

Now, for the very first time, the fully updated Autoimmune Protocol includes complete guidance for the Transition Phase, a true foundation that helps you start strong and stay consistent.

So in this episode, I’m going to walk you through what is new in this Transition Phase, what it looks like, why it matters so much, and the five simple steps you can follow to make your transition to AIP completely successful.

Welcome back to the Autoimmune Wellness Podcast. I’m your host, Mickey Trescott, and this is another installment of our AIP Deep Dive series. If you tuned in for the last episode, we covered what AIP actually is, where it came from, the science behind it, and what the newest updates to the program are.

Today we’re focusing on the very first phase of that updated framework, the Transition Phase. And I’ll be honest with you, this is the part that determines whether AIP feels doable or overwhelming. After 15 years of teaching and supporting people through AIP, I can tell you that the biggest difference between success and burnout is absolutely not willpower. Its preparation.

This episode is going to give you the roadmap to start strong, pace yourself wisely and set up systems that make AIP work for your real life.

Before we get started, a heads up that nothing in this episode should be considered medical advice. Always consult your qualified healthcare provider before making any changes to your diet or your treatment plan.

[00:02:33] AIP Transition Phase in Five Steps

So what is the Transition Phase exactly? Remember that The Autoimmune Protocol is a three phase framework, transition, elimination, and reintroduction. The Transition Phase is your on-ramp. It’s where you prepare before you hit the highway.

And here’s what might surprise you— a lot of what happens during transition actually has nothing to do with food. This phase is about laying the groundwork that makes dietary change possible. It’s where you get organized. You gather information about your current habits, you clarify your motivation, and you start making gentle strategic shifts towards the Elimination Phase. You’ll be setting up your kitchen, planning your schedule, finding support, and working on those pillars, sleep, stress, and mindset, all of the pieces that make AIP realistic and sustainable.

And instead of ripping off that bandaid and changing everything overnight, which is the old, outdated philosophy, the new transition helps you build momentum gradually. And this is what’s going to make all the difference. When we give ourselves space to plan and prepare, we reduce overwhelm, we minimize the “emergency moments” when you realize you’re hungry and you’re tired and you don’t have a single thing compliant with the Elimination Phase, ready to go.

So most importantly, it’s going to give you a chance to work with your body and your life circumstances instead of against them. So think of the Transition Phase as your foundation. When you take the time to build it, not just in your pantry, but in your mindset and in your routines, the rest of the protocol is going to flow so much more easily.

[00:04:14] Step 1: Track Your Baseline Symptoms

The first step in the Transition Phase is going to be to track your baseline symptoms. So before you change anything, it’s essential to take a snapshot of where you are right now. This means writing down your current symptoms, things like fatigue, pain, digestion, brain fog, skin issues, anxiety, sleep, and energy levels, and honestly, anything else you want to track.

You can use a notebook, you can use a spreadsheet, a symptom tracking app, whatever feels simple enough that you will actually do it. And the key is consistency, not perfection. So there are tons of fancy ways, there are wearable trackers you can use.

Personally, I’m a fan of a good old fashioned notebook, I like to keep it in a certain spot, every single morning I sit down and I notate everything, and it’s just easy for me to stay organized. I know a lot of people like wearables, apps and different trackers, and so whatever is going to work for you is what is best.

Try to track for at least one to two weeks before making any changes. So you’re going to want to note your symptoms daily and add any short reflections about your energy, your mood, and your meals. This is going to help you spot patterns later on.

So you might be wondering why this is so important. When you are in the middle of AIP, change feels very slow and very subtle, and without this clear baseline, it’s easy to lose sight of your progress.

So maybe you start sleeping a little more easily through the night. Maybe your bloating doesn’t completely go away, but it improves. Maybe your mood steadies or your pain starts to soften. Without tracking, those wins can slip by unnoticed, especially when they are in areas that are not your symptoms that you are hyper aware of, which if you have autoimmune disease, I’m sure, if you’re like me, you have symptoms that you are just constantly thinking about.

I remember one of my coaching clients who had been dealing with joint pain for a very long time, and when she started AIP, she told me she wasn’t sure if anything was helping until we compared the baseline symptom journal with her current symptoms. Her pain had actually dropped from a 7 out of 10 to a 4 out of 10 in just six weeks, and that wasn’t noticeable to her because she was so focused still about what felt hard, which living life with chronic pain, even at a low grade is still hard.

So, that is the power of tracking. It gives you perspective, motivation, and proof that your effort is working.

And here is one extra tip, include both subjective and objective measures. Your energy, your pain, and your sleep quality, these are all subjective, they’re based on how you feel. But you can also track objective data like bowel habits, menstrual cycles, or how often you rely on caffeine, how often you need a pain reliever. Together, these details give you a full picture of your progress and a realistic understanding of how your body is responding.

By tracking your baseline symptoms, you then have a clear record of where you started and a roadmap for what to look for as you move into elimination. So it’s one of the simplest tools you can use and one of the most powerful, and I really encourage you to get started with this early because once you start to make changes, you can’t go back and simply remember how you felt. Having that data is incredibly powerful.

[00:07:47] Step 2: Create Your Personal Health Vision

So the next step in the Transition Phase is to create your personal health vision. This is where you are going to define “why” you are doing AIP. This is your reason for showing up.

And I’m not talking about a vague, I just want to feel better. I mean, we all do, right? I mean something specific, something that connects you back to your real life.

So some examples of personal health vision statements might include things like, “I want to wake up with less pain and be able to take a morning walk again”.

“I want to rebuild trust in my body so I can plan my days without having a fear of a flare”.

“I want to reduce my brain fog so I can think clearly and feel confident in conversations”.

“I want to have the stamina to travel and enjoy vacations without worrying so much about how I’ll feel”.

“I want to feel calm and centered even when life gets stressful”. This is one of mine.

“I want to support my body and feel more in control of my health”.

And lastly, “I want to feel strong, capable, and connected to my body. Like I’m an active participant in my own health, not just managing symptoms”.

So whatever it is, these are just some ideas. Take a few minutes to write it down, a single sentence is enough. A list of visions is enough. Your health vision becomes your anchor. So on those hard days, and trust me, you will have some, it reminds you why you’re doing this. . It also helps you measure success in a more meaningful way.

AIP isn’t just about whether your lab numbers improve or your symptoms go away. It’s about whether you can live more fully in your body again, and sometimes spoiler alert, that doesn’t, mean perfect health. When your “why” is rooted in something personal and tangible, you’re going to notice progress even in small moments.

If you want to take this even one step further, post your health vision somewhere visible, maybe on your fridge, inside your journal, or as a note on your phone. You can even record a short voice memo to yourself for encouragement on the days that you’re tempted to give up.

Remember that AIP is a learning process, it’s not a test of discipline. It’s not something we do to punish ourselves. The clearer you are on “why” you’re doing it, the easier it becomes to meet yourself with compassion and stay committed when things get tough.

[00:10:09] Step 3: Perform a Confidence Assessment

So the next step, the third step in the new Transition Phase is brand new to the updated Autoimmune Protocol, and it’s one of the most useful things you can do before moving to elimination.

It’s called a confidence assessment, and it’s essentially taking an honest check-in with yourself about how ready you are to make changes in specific areas. The goal isn’t to pass or fail, it’s to get clear on what is already working for you and what might need extra support before you begin.

Ask yourself these questions and rate your confidence in each area on a simple scale from 1 to 10. 1 meaning you’re not confident at all, and 10 meaning I’ve totally got this handled. So here are some areas to assess, and you can also create some new areas for yourself if you want.

First is time and scheduling. Do you have time to shop, cook and plan simple meals each week? If not, what could help? Batch cooking, grocery delivery, or setting aside a weekend prep session.

Next, kitchen setup and ingredients. Do you have basic tools and pantry staples for AIP cooking? Things like oils, broth, herbs, and proteins. Do you have pots, pans? Do you have a sharp knife? Do you have a cutting board? These are going to be essential.

Cooking skills. Are you comfortable preparing simple meals from scratch? If not, could you start by practicing a few easy recipes before elimination begins?

Meal planning and organization. Do you know what you’ll eat for breakfast, lunch, and dinner during the first week? How do you use these practices in your life if you use them at all? And are you confident in organizing and meal planning and preparing ahead for food? And if you’re not someone that has ever had to do that, that’s fine, but it might be something that you have to learn how to do.

Next is your support system. Do you have emotional and physical support? So this could be family, friends, it could be an online community. Some of these supporters could be people that could actually be helping you in your home, like your partner or a family member or a friend. Others could be emotional support, like people in a Facebook group or a disease-specific group, a Reddit thread that have your similar condition and have experience with AIP. These are people who can encourage you and help you talk things through when things get hard.

Mindset and motivation. How are you feeling about starting AIP? Are you excited, nervous, motivated? Are you feeling unsure? This is just as important as the meal plan.

Energy and capacity. Do you have enough energy right now to take on a new challenge? Or do you have stuff going on in your life that is taking a lot of your attention? If not, is there anything you can do to simplify before you begin maybe pausing other commitments or asking for help? Obviously everyone has different life circumstances and some things can’t be changed, but sometimes things can be, and that’s under our control.

So once you’ve gone through these areas, notice where your confidence is high and where it’s lower. Now, those low confidence areas are the ones that I want you to pay attention to. They are going to generate an action list and show you exactly where to plan extra support before moving forward.

I like to remind people that being successful on AIP is about 50% food and 50% systems. You do not need to be perfect, but you do need a plan that fits your real life and everyone’s real life is completely different.

When I first started AIP, I didn’t realize that my biggest barrier wasn’t motivation. It was actually energy. I have Hashimoto’s thyroiditis, and I was struggling with extreme fatigue due to that. The daily task of prepping and cooking was seriously getting to me. And honestly, you guys, I was a personal chef. This was my job, I knew exactly how to do it. I could not predict the days that I would not feel well enough to cook, and so I had to develop a plan that involved help in key areas, from friends and supporters.

I started batch cooking and I started stocking pre-cooked and frozen meals for those high fatigue days. And that is what changed everything for me, from being able to go from a white knuckle, motivation only, I just have to get through it perspective, to I have myself set up, even though I don’t feel great and I’m still going to stick to this plan.

That’s what this step is really about. It’s designing a system that supports you. When your environment and your routines work with you instead of against you, AIP becomes far more sustainable and a lot less stressful, and dare I say, sometimes if you really do well here, it might even feel easy. I know some people might get mad at me for saying that.

[00:14:58] Step 4: Choose Your Start Date

Once you know which areas you’ll need to strengthen from your confidence assessment, it’s time for the next step. And that’s going to be choosing your start date.

So it might seem like a small step, but it’s actually a very powerful act of commitment. Picking the date makes your decision to start the Elimination Phase real. It’s you saying, I am ready to take this next step and put it on the calendar.

But before you do this, you need to take an honest look at the confidence scores that we just discussed. Where do you feel shaky and how long is it going to take you to improve confidence in those areas?

So maybe it’s meal planning, cooking skills, or support at home. So ask yourself, how much time is it going to take me to raise my confidence in those areas to at least a 6 or 7 out of 10? For some people that might be like a week or two of planning and practice. For others, it might take a month or even several months. No shame in taking a long time to transition.

What really matters is that you give yourself the space you need to feel ready and not rushed. So the Transition Phase is designed to be flexible on purpose. The more intentional you are with your prep, the smoother elimination will feel when you get there. Each week you spend building systems, stocking your kitchen or finding support is an investment that will pay off later in confidence, energy, and calm.

I like to recommend avoiding starting The Autoimmune Protocol during times of high stress or major life transitions. This is going to be right before a big trip, in the middle of a move, during the holidays, or when your work or family demands are especially heavy.

The Elimination Phase takes focus and consistency, and trying to do that during an already chaotic season often leads to frustration. Unless you have high motivation and strong support, like a partner that helps with meals or an AIP Certified Coach guiding you through the process, it’s usually best to wait until life feels a little steadier.

You’re going to get better results when your attention isn’t divided and your systems are in place. That being said, you can’t always predict the perfect time to start. Life rarely clears the path completely, and there’s almost always going to be something like a busy week, a family event, or an unexpected stressor that pops up right after you started. They definitely happen, and they’re going to be competing for your attention.

That’s okay, you don’t need everything to be perfect. You just need to plan well enough for those challenges so that they don’t throw you off course. If something unexpected does come up, like a flare of your autoimmune disease, a stressful deadline, a social event, you can adapt instead of abandoning the process.

So maybe that means relying on simple meals that you’ve prepped ahead, taking a night off to rest, or reminding yourself that a few hard days are not going to erase your progress.

If life feels full right now, it doesn’t mean you can’t begin preparing. You can still make progress in small meaningful ways. Practice a few elimination-friendly meals. Start improving your sleep routine or clean out your pantry. Every step you take now raises your confidence and brings you closer to readiness.

When things calm down, you’ll already be halfway there with habits forming and a foundation that makes the next step feel far more manageable. And when you do pick that start date, treat it as a promise to yourself, not for perfection, but for curiosity, consistency and trust in your own process.

[00:18:32] Step 5: Take Action on Preparation Tasks

Finally, step five, take action on those preparation tasks. This is where all the planning you’ve done starts to take shape. The goal here isn’t to overhaul everything at once. It’s to take deliberate action that strengthens the areas where your confidence was lowest, as evidenced on that confidence assessment. Every bit of progress you make now builds the foundation for a smoother, more successful Elimination Phase. Here are some focused ways to troubleshoot and take action in each area of that confidence assessment.

So first, time and scheduling. If time feels like your biggest barrier, start by mapping out your week. Identify one or two realistic blocks of time for grocery shopping and meal prep and protect them like appointments. This is not things you’re going to be fitting in, as you go about your day, there are actually devoted parts of your week that you need to have structured support.

Batch cooking, proteins or soups, using grocery delivery or prepping vegetables ahead can turn a chaotic week into a predictable routine. Even one hour of prep can save hours later.

Second, kitchen setup and ingredients. If your kitchen isn’t AIP-ready yet, don’t try to do it all in one day. Work in small zones, one drawer, one shelf, one section of your fridge at a time. Clear out expired or non-AIP staples and restock with versatile basics like olive oil, coconut milk, broth and canned seafood.

Having the right tools and ingredients in reach turns cooking from a chore into a system. And I’m not going to get into this in detail here, but you do not need to go buy a bunch of fancy, expensive kitchen equipment. You can do AIP on a very minimal set of cooking gear that none of it is specialty, and I guarantee most people already have in their kitchen.

Three is cooking skills. If cooking is intimidating, think repetition over variety. Maybe take a cooking class, watch some videos online of cooking instruction. Just the basics. You don’t need to learn anything fancy. Cook two or three simple recipes and practice them until they feel easy and doable.

Things like sheet pan meals, soups, and slow cooker recipes If you have a slow cooker. Don’t need to get one. These are all going to be your allies. As your confidence grows, you can add new dishes gradually. So the goal is consistency, not perfection or culinary creativity.

Next, meal planning and organization. Some people find meal planning completely overwhelming, so you might want to start small. Pick five, go-to meals that you enjoy and rotate them. You don’t need to have a library of hundreds of recipes in your repertoire. Just pick a few and make them over and over. Write them on a sticky note or a digital planner for quick reference and organize when you’re going to cook what. When life gets busy, repetition is your friend and it saves mental energy and it prevents decision fatigue.

Support system. If you don’t have a strong support yet, start building it now. Let friends or family know what you’re doing and why it matters. I can’t emphasize this enough. I had so many people who cared about me and my original illness and transition to AIP, and I found the biggest barrier to getting support was that actually that I just didn’t talk to certain people, and share what I was going through. Of course, we don’t want everyone to know what we’re going through, but there were certain people that ended up really helping me in specific ways that I wished that I had reached out to sooner.

So asking for that specific help, maybe somebody else cooking a meal a week, or joining you for prep day as a supporter. You can also join an online AIP community or work with an AIP Certified Coach for accountability and guidance. Support is what turns that willpower and motivation into teamwork, and that might actually help you get everything done.

Next mindset and motivation. So if your motivation is low or inconsistent, revisit your health vision from step two. Remind yourself why this matters to you. Be sure to revisit that message that you recorded to yourself on your phone. When you reconnect with that purpose, motivation will follow.

Next, energy and capacity. If low energy is your main struggle, prioritize recovery before adding new habits and really think about how to maximize your limited use of energy. As that energy stabilizes, small wins like prepping breakfast the night before or taking a short walk, build momentum naturally.

You want to work with your body when you have energy and you want to rest when you don’t have energy. And this can be one of the hardest things to troubleshoot, but hopefully it gets better as you start feeling improvements over time.

So wrapping up, in every area we talked about so far, you want to think about modifying those barriers before they become a problem.

Every meal that you prep, every night of good sleep you get, every system that you put in place, all that time that you spend getting your pantry and your kitchen set up or finding some favorite recipes, they are small investments in that future self that is going to be going through AIP, and they’re all going to add up.

By the time you reach the Elimination Phase, you’re going to have that structure, confidence and clarity. A plan that feels realistic instead of restrictive, and it makes the difference between burnout and success.

[00:24:04] Common AIP Transition Phase Pitfalls

So before we wrap up, I’m going to talk about some common pitfalls I see during the Transition Phase and how you can avoid them.

Pitfall number one. Thinking that you have to do everything at once. Now this is the old school method that I’m so happy we are done with. You do not have to do everything at once. Gradual change is sustainable change.

When people try to overhaul everything overnight, their pantry, their schedule, their sleep, their stress tomorrow… I mean, how many of us say I’m going to start Monday and it’s going to be perfection. This always leads to burnout.

Instead, focus on one or two areas at a time. Maybe this week you start tracking those symptoms and you clean out your fridge, and then next week you adjust your bedtime and you try one new AIP recipe. These small, consistent steps add up far faster than big exhausting ones.

Pitfall number two. Believing that spending a lot of time in transition is wasting your time and delaying your progress. It is absolutely not. The Transition Phase is essential to The Autoimmune Protocol, and it is an investment in your success.

Every hour you spend now building those routines, planning meals, organizing your kitchen, this is time that you are going to save later when elimination begins. And most people who struggle during The Autoimmune Protocol Elimination Phase either skip or rush transition, and then they find themselves overwhelmed when real life hits. Transition isn’t delay, it’s a foundation. So the more that you prepare now, the smoother everything else is going to feel.

Pitfall number three. Waiting for the perfect time to start. That moment will never come, life doesn’t pause for us to get healthy. There will always be something competing for your time and for your energy. What matters most is starting where you are with what you have and doing what is manageable right now. So you want to build that momentum from your action, not ideal circumstances.

And there’s one more pitfall that is worth mentioning. Number four, treating AIP like a test of willpower. This is absolutely not about being good or perfect. AIP is a tool for you to learn about your body. When something doesn’t go as planned. And let me tell you, that’s going to happen. You’re going to miss a meal prep session. You’re going to accidentally eat a food that’s non-AIP. You need to see this as information and something that you’ve learned and not failure.

The goal is progress and never perfection. AIP is about curiosity, awareness, and compassion towards yourself. The more gently and thoughtfully you move through this phase, the more confident and empowered you will feel heading into elimination.

[00:26:42] Wrap Up and AIP Foundation Series

Okay, so let’s recap what we covered today. The Transition Phase is your foundation for success with AIP. It’s where you prepare mentally, emotionally, and logistically for the challenges ahead.

Here are the five steps, again. One, track your baseline symptoms. Two, create your personal health vision. Three, perform a confidence assessment. Four, choose your start date. And five, take action on your preparation tasks.

So if you take your time with this phase, whether it’s two weeks or two months, or even more, you’ll enter elimination with confidence, clarity, and systems that support you. One of the biggest improvements to the updated Autoimmune Protocol is that we now recognize just how essential this phase really is.

So in those early days, which I’ve discussed a few times throughout this, people often jumped straight into that elimination without this prep, and it left everyone feeling overwhelmed, burnt out, and confused about what to do next. Now we know better, and you can benefit from that. Thoughtful transition is what turns AIP from something that feels restrictive into something that’s empowering, giving you a clear plan, realistic expectations, and the tools to actually sustain the process, not just for a few weeks, but for the long run.

If today’s episode helped you get a clearer idea of how to prepare for AIP, make sure you’re subscribed so you don’t miss the next episode where we’ll dive into the Elimination Phase, what to eat, what to avoid, and my best tips for making it easy, and how to stay nourished without feeling deprived.

And if you’d like some printable AIP resources to get started right away, you can download them for free in my AIP Foundation series at theautoimmuneprotocol.com/foundations. You can also find the link in the show notes.

Thanks so much for joining me today. You’ve got this, and I’ll see you next time.