Below is the full transcript of Episode 84 of the Autoimmune Wellness Podcast. This transcript is provided for accessibility and reference.

Title: Troubleshooting AIP: How to Identify What’s Going Wrong | Deep Dive (Ep 081)

Mickey: When people start the Autoimmune Protocol, they often expect the process to be fairly straightforward. You remove certain foods, focus on nutrient-dense meals, work on the lifestyle foundations, and over time you start to see improvements.

And for many people, that’s exactly what happens. But for others, things don’t unfold quite so neatly. Maybe you start the elimination phase and suddenly feel worse instead of better. Maybe you’ve been diligent for a couple of months and you’re not seeing the progress that you expected. Or maybe you’ve made it to reintroductions and you’re feeling confused about what your body is telling you.

If you’ve ever found yourself wondering, what am I doing wrong, or why isn’t this working for me, you’re not alone. Autoimmune disease is complex, and even with a well-designed protocol like AIP, it’s normal to run into obstacles along the way. That’s where troubleshooting comes in.

Troubleshooting is simply the process of stepping back, identifying what might be getting in the way of your progress, and making thoughtful adjustments so that you can keep moving forward. It doesn’t mean you failed, it just means that you’ve encountered a bump in the road that needs a little attention.

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Mickey: Welcome back to the Autoimmune Wellness Podcast. I’m your host, Mickey Trescott, and today’s episode is a Deep Dive into troubleshooting the Autoimmune Protocol. Over the years, I’ve seen thousands of people implement AIP through my books, courses, and coaching programs, and one thing I can tell you with certainty is that almost everybody needs to troubleshoot something at some point.

It’s simply a part of the process when you’re working with a healing protocol in the context of real life. Because troubleshooting is just this massive topic. I’m planning a series of episodes that will explore different challenges people run into while implementing AIP. We’ll be looking more deeply at issues like feeling worse when you start the protocol, struggling with compliance or sustainability, lack of progress after the elimination phase, digestive challenges, and navigating the reintroduction process.

But before we dive into those more specific topics, I wanted to create an overview episode that explains just how troubleshooting works in general. Think of this episode as the big picture view. We’re going to talk about when it makes sense to troubleshoot, when it doesn’t, the most common types of challenges that people run into during the transition elimination and reintroduction phases and how to approach the troubleshooting process in a way that is thoughtful and methodical rather than overwhelming.

So if you’ve been feeling stuck, confused or discouraged at any point in your AIP journey, my hope is that this episode will help you step back, look at the situation with more clarity and identify the next step that might help you forward.

And before we get started, as always, a quick reminder that this podcast is for informational and educational purposes only and is not intended as medical advice. Always consult your healthcare provider before making any changes to your diet, lifestyle, or treatment plan.

[00:03:05] What Troubleshooting Actually Means

Mickey: Okay, let’s dive into troubleshooting the Autoimmune Protocol, and before we start talking about specific problems that can come up during AIP, I want to take a moment to clarify what troubleshooting actually means in this context. When you hear the word troubleshooting, you might assume that it means something has gone wrong or that the protocol isn’t working, but that’s not really how I think about it.

I like to think about AIP as a road trip. You have mapped out your destination; better health, improved symptoms, more stability with your autoimmune condition, and the protocol gives you a clear route to follow to get there. But just like any long trip, the road isn’t always perfectly smooth. Sometimes there’s traffic, sometimes there’s construction.

Maybe you hit bad weather or you have to stop to fix a flat tire. None of those things mean that your whole trip has failed. They simply mean you need to pause, reassess, and make a small adjustment so that you can keep moving in the right direction.

Troubleshooting is that process of reassessing and adjusting, and the reality is that most people will need to do some form of troubleshooting during their time implementing AIP. That’s not a reflection of failure on your part. It’s simply what happens when a structured protocol meets the complexity of your real life and the complexity of your actual body.

And over the years in my work with the AIP community, I’ve seen many of the same challenges appear again and again. People run into issues with maintaining compliance or they feel overwhelmed by the logistics of cooking and planning meals. Other people experience new digestive symptoms when they dramatically change their diet.

Some people do everything carefully for about a month or two, and then they feel really discouraged when they don’t see the improvements they were hoping for. And sometimes there are even underlying medical factors. So these are things like infections, nutrient deficiencies, hormonal issues or even other health conditions that need to be addressed alongside diet and lifestyle changes.

All of these situations fall under the umbrella of troubleshooting. What’s important to understand is that troubleshooting is most effective when it’s done methodically. When something doesn’t feel right, it’s very tempting to start changing a lot of little things at once. Ask me how I know! People might begin removing additional foods, layering in multiple new supplements, or jumping from one strategy to another in quick succession. But that approach often creates more confusion instead of clarity.

Instead, the goal of troubleshooting is to slow down, identify the most likely cause of the problem, and make one thoughtful adjustment at a time so that you can observe how your body responds. Another important point is that troubleshooting doesn’t always mean making the protocol stricter. In fact, many of the issues people run into during AIP are caused by the opposite. Moving too quickly, not eating enough or trying to power through this process using willpower alone instead of building sustainable habits.

So sometimes the solution is to actually just simplify or slow down rather than add more layers. So as we move through this episode, I want you to keep that bigger perspective in mind. Troubleshooting isn’t about searching for something that you’ve done wrong. It’s about learning how to respond to the feedback your body and your life circumstances are giving you so that you can continue moving forward in a sustainable way.

[00:06:32] When It Makes Sense to Troubleshoot — and When It Doesn’t

Mickey: Next, let’s talk about an important distinction, when it actually makes sense to begin troubleshooting and when it’s better to stay the course and give the process just a little more time. One of the most common patterns I’ve seen over the years is people either jumping into troubleshooting way too early, like me making millions of changes before I really understand what’s going on, or waiting far too long while something clearly isn’t working.

So understanding the timing can make a big difference. Let’s start with situations where troubleshooting makes a lot of sense. A good time to begin troubleshooting is when you notice something that is clearly interfering with your ability to move forward with the protocol. For example, if you are struggling to maintain compliance with the elimination phase, maybe you keep starting and stopping, or you’re relying entirely on willpower just to get through one day at a time.

That’s a sign that something about your plan needs to be adjusted. Another situation where troubleshooting is helpful is when new symptoms appear after starting AIP, especially if they’re significant or persistent. While it’s very normal for your body to go through some mild adjustments when you change your diet, you shouldn’t feel dramatically worse, or like you have to push through severe symptoms to make it work.

Troubleshooting can also become important if you’ve spent 30 to 90 days in the elimination phase, you’ve been consistent and you’re not seeing the progress that you expected. Now, this doesn’t necessarily mean the protocol isn’t helping, but it might mean that there are other factors that need attention. And finally, troubleshooting often comes into play during the reintroduction phase. This is the most nuanced stage of AIP, and it’s very common for people to feel uncertain about what their reactions mean, whether they are moving too quickly or whether something outside of what they’re eating is affecting their symptoms.

In all of these cases, troubleshooting helps you pause, gather information, and make thoughtful adjustments before continuing. So let’s talk about when not to troubleshoot. The most common mistake I see is people starting to troubleshoot too early, especially during those first few days or weeks of transitioning to AIP.

When you make major changes to your diet and your lifestyle, your body often needs time to adapt. So if you start removing foods, increasing vegetables, shifting your macronutrient balance, and changing your routine all at once, it’s normal to notice some temporary adjustments. So if you begin troubleshooting immediately at that first sign of discomfort, you can end up overcomplicating the process before giving the protocol enough time to work.

Another situation where troubleshooting can backfire is when you start layering additional restrictions too quickly. For example, adding low FODMAP, low histamine or other restrictive diets on top of AIP right from the beginning without first seeing how the basic protocol works for your body. While there are situations where those approaches are appropriate, adding them to soon can create unnecessary complexity and overwhelm.

In general, troubleshooting works best when you allow the protocol enough time to establish a baseline, observe what’s happening, and then make targeted adjustments if something truly isn’t working. In other words, a goal isn’t to constantly be tweaking throughout the process. It’s to respond thoughtfully when a genuine obstacle appears.

[00:09:51] The Three Layers of Troubleshooting

Mickey: And once you recognize that it’s time to troubleshoot, the next step is understanding what category the problem might fall into, because not all challenges during AIP come from the same place. In the next segment, we’re going to look at the three broad layers where the most troubleshooting issues tend to occur, implementation challenges, physiological adjustments, and underlying medical factors.

[00:10:15] Layer One: Implementation Challenges

Mickey: The first layer is implementation. In other words, how the protocol is actually being carried out in real life. This is by far the most common source of problems . AIP asks you to make significant changes to the way that you shop, cook, eat and structure your routine. That’s a big shift, and sometimes the challenges that you might run into are simply related to the logistics of implementing those changes.

For example, you might move into the elimination phase before you are fully prepared, which can make it hard to maintain compliance. Other people might be relying entirely on willpower instead of building systems that support their new way of eating. Things like meal planning, batch cooking, or having supportive people around them.

Sometimes the issue is sustainability. So you might technically be following the elimination phase, but then you might actually feel exhausted by the effort that it takes every day, counting the days until it’s over. That’s a sign that something about the approach needs adjustment so that it becomes more manageable.

And another common implementation issue is focusing too much on what’s removed instead of what is added. AIP isn’t just about eliminating foods, you should all know this by now. It is also about prioritizing nutrient dense foods that help support healing. So somebody is simply removing foods, but not actively building nutrient-dense meals, they might not experience the full benefits of the protocol.

So before assuming there’s something medically complex going on, it’s always the first thing we jump to, right? It’s always worth taking a step back and asking, is the protocol being implemented in a way that is consistent, sustainable, and nutrient dense?

[00:11:58] Layer Two: Physiological Adjustments

Mickey: Now the second layer involves how the body adapts to dietary and lifestyle changes. When somebody shifts their diet significantly, so maybe you are increasing your vegetables, changing the level of carbohydrates that you eat, incorporating new fats, or introducing foods that you haven’t really eaten before, your body sometimes needs time to adjust.

For example, some people might experience fatigue or headaches early on if they’re not eating enough carbohydrates for their needs. Others might notice digestive changes as fiber intake increases, or as their body adjusts to a different balance of fats and proteins. It’s also possible to discover that certain foods included on AIP don’t work well for you personally, and this is actually very common. Coconut is probably the best example here. It’s included in the elimination phase, but a lot of people find they react to it and need to leave it out.

These kinds of adjustments are fairly common. They usually don’t require a complete overhaul of the protocol. Instead, troubleshooting might involve slowing down the transition, adjusting those macronutrients, modifying the intake of specific foods, or allowing your body more time to adapt.

One important misconception I like to address here is this idea of a “detox phase”. There’s a narrative in some wellness spaces that you should expect to feel terrible when you start a healing diet. That feeling worse is somehow a sign that your body is detoxifying or doing the right thing. In reality, that’s not how AIP works. While mild adjustments as you are changing and shifting things are very normal, feeling significantly worse is usually a signal that something needs to be adjusted rather than pushed through.

[00:13:41] Layer Three: Medical Complexity

Mickey: The third layer is underlying medical factors. So for some people, diet and lifestyle changes alone aren’t enough to fully address what’s going on with their health. There might be other factors involved that require medical investigation or treatment. These include things like nutrient deficiencies, hormone imbalances, chronic infections, environmental exposures, or other conditions that affect immune function.

In these cases, AIP can still play a powerful supportive role, but it may need to be combined with appropriate medical care. This is one of the reasons I always encourage people implementing AIP to maintain a collaborative relationship with their healthcare providers. Diet and lifestyle can be incredibly powerful tools, but they are not meant to replace medical care when it’s needed.

Thinking about troubleshooting in these three layers helps bring structure to the process. Instead of assuming the most complicated explanation right away, you can move through each layer methodically, starting with implementation, then considering those physiological adjustments and finally exploring deeper medical factors if necessary. And once you understand these layers, it becomes much easier to recognize where challenges tend to appear during each phase of AIP.

[00:14:57] Troubleshooting Within Each Phase of AIP

Mickey: So next we’re going to look at some of the most common types of problems people encounter during the transition phase, the elimination phase, and the reintroduction phase.

[00:15:07] Transition Phase Troubleshooting

Mickey: you already know that each of these phases has its own goals, and because those goals are different, the types of obstacles that come up tend to look different as well. The transition phase is the preparation period before beginning the elimination phase. Now the goal here is not perfection, it’s building the foundation that will make elimination achievable and sustainable.

Interestingly, this phase did not originally exist in the early days of AIP. When the protocol first formed more than a decade ago, most people were encouraged to just jump straight to that elimination. The assumption was that if you were motivated enough, you could just start eliminating foods and figure things out along the way. And for some people that worked, but for many others it didn’t.

Over time, it became very clear that one of the biggest reasons people struggled with AIP wasn’t the dietary framework itself, it was the lack of preparation before starting, people would jump into elimination without having any of the skills, systems or support in place to sustain such a big change. That experience was a big part of why AIP eventually evolved to include a formal transition phase.

Now, the modern transition phase is essentially designed to presolve the barriers that commonly derail people during elimination. And most of the troubleshooting issues that arise during this phase stem from rushing through the preparation process. This is so understandable. Most of us come to AIP because we’re not feeling well. We want relief as soon as possible.

And when you finally discover a framework that might help, it’s incredibly tempting to just jump straight in. But when you skip important prep steps, those missing pieces often show up later as bigger problems.

One example is inadequate baseline tracking. So before beginning elimination, you have to understand what your symptoms actually look like at baseline. That might include things like your energy levels, digestion, skin symptoms, pain levels, sleep quality, or other markers relevant to your condition. Without that baseline, it becomes so much harder to tell whether the protocol is improving your symptoms or whether changes you’re noticing are related to something else.

Another common issue during transition is skipping reflection and planning exercises. So in the New Autoimmune Protocol and in episode 52 of this podcast, we talk about developing a personal health vision and assessing your confidence in different areas of implementation. These exercises might sound skippable, but they’re extremely valuable because they help you identify potential barriers ahead of time.

For example, somebody might realize they feel confident about cooking, but not about navigating social situations. Or they might feel prepared to shop and meal plan, but uncertain about how they will handle travel or work schedules. Identifying those challenges specifically for you, early, allows you to address them before elimination begins, instead of discovering them in the middle of the stressful week.

Preparation tasks also matter. That might include learning a few reliable recipes, stocking your kitchen with staple ingredients, figuring out where you’re going to source compliant foods, or asking for support from family members or partners. If those pieces aren’t in place, the elimination phase can quickly start to feel overwhelming.

So when troubleshooting issues arise during transition, the solution is usually not to push ahead faster, it’s to slow down and strengthen the prep process. Give yourself an extra week or two, maybe even a month to prepare, and that can make a huge difference in how smoothly the elimination phase unfolds.

And in many cases, that extra preparation time is exactly what allows people to successfully complete elimination and move on to reintroduction with much less stress.

[00:18:59] Elimination Phase Troubleshooting

Mickey: The elimination phase is where most people spend the bulk of their time on AIP, and it’s also where most troubleshooting tends to occur. There are several categories of challenges that commonly show up during this stage. The first is compliance. Compliance issues happen when someone intends to follow the elimination protocol, but repeatedly finds themselves unable to maintain it. This might show up as starting and stopping multiple times, accidentally consuming excluded foods or finding that life circumstances make the protocol difficult to follow.

When compliance issues arise, it’s important to step back and ask what might be getting in the way? Is the protocol being implemented too quickly? Are there unexpected stressors or responsibilities interfering with meal preparation? Are there relationship dynamics or social situations that make compliance difficult?

Sometimes the solution is education or support. Other times it’s adjusting the approach. For example, moving from core AIP to modified AIP. Simplifying meal routines or getting help from an AIP Certified Coach or practitioner.

Closely related to compliance is sustainability. This is a situation where somebody technically maintains elimination, but the process feels extremely stressful. They might feel like they’re hanging on through sheer willpower or counting the days until elimination ends, and when that happens, it’s often a signal that the current approach is not sustainable. Now, the elimination phase shouldn’t feel effortless. It is pretty hard to do, but it also shouldn’t feel like an endurance test where you’re “white knuckling” your way through every single day.

Troubleshooting sustainability might involve simplifying your meals, building more support systems, revisiting preparation steps from the transition phase, or adjusting expectations about how the protocol fits into your daily life.

Now another common category of troubleshooting during elimination involves new symptoms or negative changes. Some people experience fatigue, headaches, or digestive changes early in the elimination phase. Again, we’ve talked about this earlier, these symptoms relate to how the diet has changed. For example, you might inadvertently reduce your carb intake too much while removing all of those processed foods.

And in that situation, adding starchy AIP friendly carbs like sweet potatoes, winter squash, or plantains can often help resolve symptoms like fatigue or lightheadedness. Digestive changes again, can absolutely occur when your fiber intake increases or fat intake changes. Sometimes your body simply needs time to adjust and slowly increasing those vegetables or fats can help ease that transition.

There are also situations where somebody might react to a food that’s technically allowed. Again, we talked about coconut. When those new symptoms appear, it’s important not to assume that you need to push through them. Instead, those symptoms are useful information that can guide small adjustments.

Finally, the issue of lack of progress. If somebody has spent 30 to 90 days in elimination, maintained reasonable compliance and tracked their symptoms, but hasn’t noticed meaningful improvement, it’s time to reassess. Sometimes the issue is related to expectations or tracking methods. For example, you might focus exclusively on your primary autoimmune symptom while overlooking improvements in areas like digestion, sleep, or energy levels.

Other times troubleshooting might involve increasing nutrient density, addressing lifestyle factors like sleep or stress, or collaborating with your healthcare providers to investigate underlying medical issues.

[00:22:41] Reintroduction Phase Troubleshooting

Mickey: The reintroduction phase brings a different set of challenges. At this point, people have invested a significant amount of time and effort into elimination, and there can be a lot of pressure to navigate reintroductions correctly. One of the most common mistakes I see is starting reintroductions too soon.

Ideally, reintroductions should begin only after spending 30 to 90 days in elimination and experiencing measurable improvements from baseline. Without these improvements, it becomes very difficult to determine whether a food is causing a reaction. Another frequent issue is rushing through the actual reintroduction process. Because people are excited to expand their diet, it can be tempting to move quickly from one food to the next.

But when reintroductions happen too close together, it becomes difficult to isolate those reactions. So patience is especially important here. You want to allow enough time between each reintroduction to clearly return to your improved baseline before testing the next food.

There are also situations where it’s difficult to determine whether symptoms are related to a food or to something else entirely. Stress, poor sleep, illness, intense exercises, hormonal changes, medications, environmental exposures can all influence symptoms and make reactions harder to interpret.

Another concept that comes up frequently during reintroductions is gray area foods. Now these are foods that might not cause a clear reaction every single time you eat them, but might cause symptoms under certain conditions. For example, if eaten frequently combined with other reintroduced foods, or consumed during periods of high stress or poor sleep. Discovering these patterns takes time and careful observation, which is why slowing down the reintroduction process is so valuable.

Finally, some people experience food fears or anxiety about reintroducing foods, especially if they experience significant symptom relief during elimination. While those feelings are understandable, avoiding reintroductions altogether can create long-term challenges and may even contribute to unhealthy relationships with food. The goal of AIP is not to remain in elimination indefinitely. It’s to identify the foods that support your health while expanding your diet as much as possible.

Looking at troubleshooting through the lens of each phase of AIP helps bring clarity to what might otherwise feel like a very confusing process. Different phases come with different challenges and understanding that can help you respond appropriately instead of assuming something has gone fundamentally wrong.

[00:25:19] The Mindset of Troubleshooting

Mickey: Next I want to talk about one of the most important aspects of troubleshooting: the mindset that allows you to approach these challenges calmly and methodically instead of reacting out of frustration or overwhelm.

When people run into obstacles during AIP, it’s very easy for the experience to become emotionally charged. You might feel discouraged, frustrated, or worried that you’ve done something wrong. And if you’ve been dealing with autoimmune disease for a long time, those feelings can run even deeper. Many people come to AIP after years of searching for answers, trying different treatments, and hoping that this will finally be the thing that helps.

So when something doesn’t go as expected, it can feel extremely discouraging. But one of the most helpful shifts you can make is to start thinking about troubleshooting, not as a setback, but information. Your body is constantly giving you feedback, your symptoms, your energy levels, your digestion, your sleep, your mood.

All of these are signals that tell you something about what is or isn’t working. Troubleshooting is simply the process of listening to that feedback and responding thoughtfully.

Another important mindset shift is resisting the urge to make too many changes at once. I talked about this at the beginning. When something feels off, some people have this urge to just throw everything at the problem. I’m definitely this type of person. You might remove additional foods, add a bunch of supplements, change your meal structure, and start researching a dozen possible root causes all at the same time.

But when you change too many variables simultaneously, it becomes almost impossible to determine what actually made a difference. So I’ve said this before, but the most effective approach is to slow down and make one adjustment at a time, allowing enough time to observe how your body responds.

Patience play such a big role here. Healing from autoimmune disease is rarely linear. There are often periods of improvement, plateaus, occasional setbacks along the way, and troubleshooting is a part of navigating those natural ups and downs.

And finally, it’s important to remember that you don’t have to figure out everything on your own. For some troubleshooting challenges, especially those involving complex medical issues, working with a knowledgeable healthcare provider like an AIP Certified Coach can be incredibly helpful. They can help you interpret symptoms, decide when testing might be appropriate, and guide you through the next steps.

[00:27:41] Wrap-Up and Closing

Mickey: And that brings me to the big takeaway from today’s episode. Needing to troubleshoot during AIP is not unusual. In fact, for many people it’s an essential part of the process. When I look back at my own experience, the truth is that most of my time on AIP wasn’t smooth sailing. It was actually troubleshooting.

Yes, there were moments of incredible progress, but there were also long stretches where I felt stuck, confused or unsure about what to do next. I had to investigate digestive issues, adjust how I was eating, I had some infections, I worked with many practitioners, and I slowly uncovered layers of what was going on in my body.

And at the time, I remember feeling frustrated. I remember thinking, why is this so complicated? But looking back now, I can see that every one of those troubleshooting steps helped me understand my health more clearly. Each adjustment brought me a little bit closer to what my body actually needed, and that’s often how healing with autoimmune disease works. It’s not just a single switch that flips everything into place. More often, it’s a process of learning, adjusting, and refining over time.

In the upcoming episodes, I’m going to go much more into depth about some of the most common challenges people encounter, but for now, if you’re in a place where things feel confusing or stuck, I hope this overview has helped you take a step back, see that troubleshooting isn’t a sign that something has gone completely wrong. It’s just a part of learning how your body responds.

And if you’re listening to this in real time, we are just about to begin our guided transition inside the pre-order community for the New Autoimmune Protocol. This is where I will be walking you step by step through the transition phase so that you can prepare for AIP in a way that avoids many of the common pitfalls we talked about today.

We are just about to get started, so if you’ve been thinking about joining, now is the time to jump in so you don’t miss it. Head over to theautoimmuneprotocol.com/preorder to get access and join us. And after this guided transition, we’re going to be moving into a full group AIP together in June, once everybody has their books in hand. So this is really your chance to get set up and go through the process with support from me from the very beginning.

Thank you so much for listening to the Autoimmune Wellness Podcast. If you found this episode helpful, feel free to share it with someone who might benefit from it as well.

And as always, take good care of yourself and I’ll see you in the next episode.