Elimination, Core & Modified: Phase 2 of the Autoimmune Protocol | Deep Dive (Ep 053)

Episode 53: Elimination, Core & Modified – Phase 2 of the Autoimmune Protocol

For many people, the Elimination Phase is what comes to mind when they think about the Autoimmune Protocol—but it’s also the most misunderstood part. Conflicting food lists, outdated advice, and fear of restriction have left many people unsure how to approach elimination in a way that’s effective and sustainable. In this episode, Mickey clarifies what the Elimination Phase actually looks like today, following the 2024 update to the Autoimmune Protocol.

As part of the AIP Deep Dive series, this episode focuses on Phase 2 of the updated framework: the Elimination Phase. Mickey explains why elimination is meant to be temporary, how it fits into the larger AIP process, and how the introduction of Core AIP and Modified AIP makes the protocol more accessible without compromising its effectiveness.

This episode provides a clear, practical roadmap for navigating elimination with confidence—covering what to remove, what to include, how long to stay in this phase, and how to troubleshoot common challenges—so you can move forward without overwhelm or guesswork.

In this episode, you’ll learn:

1. What the AIP Elimination Phase is—and what it isn’t
2. Why elimination is a temporary learning phase, not a lifelong diet
3. How Core AIP and Modified AIP differ and why both exist
4. Which foods are avoided on Core AIP
5. Which foods are included on Modified AIP and why
6. What foods to focus on adding for nutrient density and healing
7. How long the Elimination Phase typically lasts
8. How to troubleshoot fatigue, cravings, digestive changes, and overwhelm
9. Practical meal planning and batch cooking strategies to make elimination easier

Resources:

1. AIP Foundation Series – Free 5-day email course with printable food lists, meal plans, and beginner resources.
2. AIP Certified Coach Program & Practitioner Directory – Advanced training for licensed healthcare providers and a worldwide directory to find AIP-trained support.

Episode Timeline:

00:00 – Introduction to the Elimination Phase and AIP updates

02:38 – What the Elimination Phase is—and isn’t

04:18 – Core AIP vs. Modified AIP explained

06:20 – Foods to avoid on Core AIP

11:05 – Foods included on Modified AIP

15:29 – Foods to include on both Core and Modified AIP

20:17 – How long to stay in the Elimination Phase

23:32 – Troubleshooting symptoms during elimination

27:57 – Meal planning and batch cooking strategies

32:18 – Wrap-up & AIP Foundation Series