Troubleshooting AIP: How to Identify What’s Going Wrong | Deep Dive (Ep 084)

When you start the Autoimmune Protocol, it’s easy to expect a fairly straightforward path: remove certain foods, focus on nutrient density, support your lifestyle—and over time, feel better.

And for some people, that’s exactly what happens.

But for many others, the process feels more complicated. You might feel worse when you begin, struggle to stay consistent, stop seeing progress after a few months, or feel confused during reintroductions.

If you’ve ever wondered, What am I doing wrong? or Why isn’t this working for me?—you’re not alone.

In this episode of the AIP Deep Dive series, Mickey introduces troubleshooting as a normal and essential part of the process. Rather than seeing obstacles as failure, this episode reframes them as useful feedback—and gives you a clear way to identify what might be getting in the way and how to move forward.

Mickey explains when it actually makes sense to troubleshoot (and when it doesn’t), outlines the three main layers where issues tend to arise, and walks through how to make thoughtful adjustments without creating more confusion.

1. What troubleshooting really means—and why it doesn’t mean you’ve failed
2. When to troubleshoot vs. when to give the process more time
3. The three layers of troubleshooting: implementation, physiology, and medical factors
4. Common challenges in each phase (transition, elimination, and reintroduction)
5. Why lack of progress after 30–90 days may require a different approach
6. How to avoid overcomplicating the process with too many changes at once
7. Why mindset and patience play a key role in long-term success

1. The New Autoimmune Protocol (Book) – A practical guide to implementing AIP with a focus on preparation, sustainability, and personalization
2. AIP Foundation Series – Free 5-day email course with food lists, meal plans, and beginner tools
3. Episode 52: Tracking & Preparing for AIP

Episode Timeline:

00:00 – Why AIP doesn’t always go as expected

03:05 – What troubleshooting actually means

06:32 – When to troubleshoot—and when not to

09:51 – The three layers of troubleshooting

10:15 – Implementation challenges

11:58 – Physiological adjustments

13:41 – Underlying medical factors

14:57 – Troubleshooting across AIP phases

15:07 – Transition phase challenges

18:59 – Elimination phase troubleshooting

22:41 – Reintroduction phase challenges

25:19 – The mindset of troubleshooting

27:41 – Key takeaways and closing