Episode 69: Core vs. Modified AIP Elimination Phase — How to Choose | Deep Dive

If you’re learning about the Autoimmune Protocol for the first time—or revisiting it after trying it years ago—one question almost always comes up during the Elimination Phase:

Should I start with Core AIP or Modified AIP?

It sounds like a simple choice, but for many people it feels loaded. Some wonder which version will “work better.” Others worry about sustainability, cost, cultural fit, or whether they can realistically maintain the structure long enough to see results.

In this episode of the AIP Deep Dive series, Mickey breaks down the key differences between Core and Modified AIP, explains why both versions exist, and walks you through how to decide which one is the best fit for you right now. Rather than framing the choice as a matter of willpower or commitment, this episode reframes it as a question of context, sustainability, and nutrient density.

Mickey also discusses who each version tends to work best for, what the research currently says (and doesn’t say), how Modified AIP evolved from real-world use, and how to transition between versions if needed.

In this episode, you’ll learn:

1. Why the Core vs. Modified question exists today
2. What is removed on Core AIP and how it differs from Modified
3. Which foods are included in Modified AIP and why
4. Who Core AIP tends to work best for
5. Why Modified AIP is now the recommended starting point for most people
6. How accessibility, affordability, and cultural relevance factor into your decision
7. The research reality behind both versions
8. Why nutrient density matters regardless of which version you choose
9. How to transition from Modified to Core if needed
10. Why fit and sustainability matter more than perfection

Resources:

Referenced Episodes:

1. Episode 53: The Elimination Phase Explained (Deep Dive)
2. Episode 55: Nutrient Density & Lifestyle Changes – Essential to All Phases of AIP

AIP Foundation Series – Free 5-day email course with printable food lists for both Core and Modified AIP, reintroduction charts, meal plans, and beginner tools.

The New Autoimmune Protocol (Book) – The first AIP resource built to reflect the updated Modified AIP framework while prioritizing nutrient density and therapeutic principles. Available for pre-order wherever books are sold.

Episode Timeline:

00:00 – Core vs. Modified: why this question matters

02:16 – Elimination Phase overview at a glance

03:21 – What is removed on Core AIP

04:07 – What’s included on Modified AIP

05:09 – Timeline reminder & Foundation Series reference

06:21 – Why Modified AIP was created

08:30 – Who Core AIP tends to work best for

10:36 – Why Modified AIP is recommended for most people

11:38 – Accessibility & affordability considerations

12:27 – Modified AIP for vegetarians, active individuals & weight restoration

14:28 – The research reality: what we know and what’s next

16:22 – The biggest tradeoff: nutrient density

18:39 – What happens to existing Core AIP resources

20:47 – A note on known sensitivities

21:54 – Cultural relevance and making AIP your own

23:40 – Transitioning from Modified to Core

25:33 – Closing recap & book pre-order

If you're learning about the Autoimmune Protocol for the first

time, or revisiting it after trying it years ago, there's one question

that almost always comes up when people reach the Elimination Phase.

Should I start with Core AIP or Modified AIP?

And it sounds like a simple choice, but for a lot of people,

they're just not so sure.

Some aren't sure which version makes the most sense for their body or

their lifestyle, and others have tried Core AIP in the past and are

wondering whether there's another way to approach elimination that

feels more doable this time around.

What often gets lost in that question is this: both versions of

the Elimination Phase exist for a reason, and choosing between them

isn't about willpower or commitment.

It's about fit.

Today's episode is about helping you understand the differences between

Core and Modified AIP, and more importantly, how to decide which one

is the right place for you to start.

Welcome back to the Autoimmune Wellness Podcast.

I'm your host, Mickey Trescott, and this episode is a part of our ongoing AIP Deep

Dive series, where we're walking through the Autoimmune Protocol step-by-step, with

updated guidance and real world context.

Back in episode 53, we covered the Elimination Phase as a whole, in depth.

What it is, why it works, how long it lasts, and the comprehensive food

lists for both Core and Modified AIP.

We also talked about how it fits into the context of Transition

and Reintroduction phases.

So if you are here looking for a detailed overview of the Elimination Phase itself,

definitely head back to episode 53 because that's the best place to start.

Today we're going to talk through how to choose between Core and Modified AIP, who

each version tends to work best for and why the version that is "right" for you

is the one that you can actually sustain.

And before we begin, a quick reminder that this podcast is for educational

and informational purposes only.

It is not intended as medical advice, and it's not a substitute for care

from your healthcare providers.

So please make any dietary or lifestyle changes in partnership

with your medical team.

Before we talk about how to choose between Core and Modified AIP, I want to give

you a short, big picture overview of what the Elimination Phase actually looks

like and how these two versions differ.

The Elimination Phase, officially phase two of the Autoimmune Protocol, is

a temporary, structured period where you remove foods that are more likely

to contribute to inflammation, gut permeability or immune activation.

While also emphasizing foods that are deeply nutrient dense

and supportive of deep healing.

Across both versions of the Elimination Phase, the foundation is exactly the same.

You are building meals around high quality proteins and seafood, a wide variety of

vegetables, especially leafy greens and colorful plants, healthy fats like olive

oil, avocado, coconut, colorful fruit, and supportive nutrient dense foods like bone

broth, fermented foods, herbs and spices.

And where Core and Modified approaches differ is in which foods are eliminated.

So on Core AIP, the Elimination Phase removes the full set of food

categories that research and clinical experience suggest are most likely

to cause inflammation or be triggers for people with autoimmune disease.

This includes all grains and gluten containing foods, dairy, eggs, legumes,

nuts and seeds, nightshades and all of the spices that are derived from them, alcohol

and highly processed food and additives.

Core AIP is the most comprehensive version of elimination.

It's the version used in all of the published AIP research, and it creates

a highly controlled environment for identifying food triggers.

If you have come across the Autoimmune Protocol in the past, this is likely

the protocol that you encountered.

Modified AIP, the newest version of elimination, keeps that same framework

and the same goal, but it allows for a small number of foods that many

people actually tolerate very well.

This makes elimination much more accessible and sustainable.

During Modified AIP, the following foods are included in contrast to Core

Rice in all forms, most legumes with the exception of peanuts and soy,

ghee, which is clarified butter with minimal dairy proteins, whole seeds and

seed-based spices, and then pseudo-grains, like quinoa, buckwheat, and amaranth.

Everything else remains the same as Core AIP during elimination.

So we're taking out eggs, dairy other than ghee, grains other than rice, nuts,

nightshades, alcohol, and processed foods.

The difference isn't about changing the purpose of the Elimination

Phase, it's about how many specific foods are removed during this phase.

And a reminder, both Core and Modified AIP are designed to be temporary.

For most people the Elimination Phase lasts 30 to 90 days.

Long enough for inflammation to settle and symptoms to stabilize, but short enough

to remain sustainable and purposeful.

And if you want the complete food lists for both Core and Modified AIP,

along with printable guides and tools to help you actually use them in real

life, you can download these for free as a part of the AIP Foundation Series.

You'll find side-by-side food lists, reintroduction charts, and all of the

other resources that make it easier to stay organized and confident

as you move through each phase.

You can get them at autoimmunewellness.com/foundations

or find the link in the show notes.

And again, if you want that full breakdown of the Elimination Phase itself,

including the detailed rationale behind each of those food categories and exact

guidance on how to move through your Elimination Phase, go back to episode 53.

I cover all of it there.

Today's episode builds on that foundation to help you decide which

version of the Elimination Phase is the best for you to start right now.

So why does this question Core AIP or Modified AIP even

exist in the first place?

For a long time, there was only one version of the AIP Elimination Phase.

What we now call Core AIP was simply just the Autoimmune Protocol.

That version formed the foundation of AIP as it was studied, taught, and

shared, and it's the version used in all of the published research to date.

It's also the version many people were introduced to when

they first learned about AIP.

But over time, something important became very clear.

With thousands of people using the Autoimmune Protocol while navigating busy

schedules, limited food access, financial constraints, cultural food traditions,

and then all of the very real energy limitations that come with chronic illness

and autoimmune disease, practitioners and coaches, healthcare providers

started seeing consistent patterns.

Some people did incredibly well on Core AIP spoiler alert--

usually people who have a lot of support and resources to do it.

Other people struggled.

And not because they lacked commitment, but because the level

of restriction created barriers that just made it really hard to sustain.

And this is where the evolution of AIP began.

Modified AIP exists because we learned from real people using AIP in real life.

We learned where the protocol was helping and where it was

sometimes getting in the way.

We learned that sustainability, accessibility, affordability, and cultural

relevance are extremely important.

And this update was not about weakening the Autoimmune

Protocol or making it easier.

It was about making it usable for more people without losing any of those core

principles that make AIP so effective.

So the goal never changed: to reduce inflammation, support immune balance,

and identify those food triggers in a structured and intentional way.

What did change was how many paths are offered to people to get there.

And that's why this question exists now because AIP has grown and matured so

much and it is now adapted to better meet people where they actually are.

Now let's talk about Core AIP and who this comprehensive version of the

Elimination Phase tends to work best for.

Core AIP, again, it's that original version of the protocol.

It's the version used in all of the published research, and

it creates the most controlled environment for calming inflammation

and identifying food triggers.

Because of that, it can be very effective, but it is also the most demanding.

Core AIP tends to work best for people who have a high degree of flexibility

and support during the Elimination Phase.

So this might look like having more control over your schedule, the ability

to cook most of your meals at home and access to a wide variety of foods.

It often works best when someone has the time, the energy, or the

resources to plan, shop, and prepare meals consistently for several weeks.

It also can be a good fit if you're in or closely resemble one of the populations

that has been studied using Core AIP.

For example, research using the Core AIP Elimination has shown a 73%

clinical remission rate in people with inflammatory bowel disease

after six weeks, and improvements in symptoms, weight, and inflammatory

markers in people with Hashimoto's thyroiditis over 10 to 12 weeks.

So if you are somebody with IBD or Hashimoto's, those results might be a

strong motivator to choose Core AIP, especially if you want to follow the same

approach that was used in those studies.

That being said, it's important to name something very clearly.

Choosing Core AIP does not guarantee it might work better.

Core AIP is simply one of two tools we have and it works

best in specific contexts.

For some, the level of restriction can increase stress, reduce consistency,

or make it harder to get enough food and nutrients, especially

if you do it for a long time.

So if you have tried Core AIP in the past and found it difficult to stick

with, that's not a personal failure.

It's just information that can help guide a better fit and choice moving forward.

Let's talk about why today I recommend Modified AIP as the

starting point for most people.

Modified AIP keeps the same framework and the same goals-- the

intention definitely has not changed.

We're still aiming to calm inflammation, support immune regulation, and create

that clear baseline so that you can learn how your body responds to food.

But the different thing is some of these barriers.

Modified AIP was designed to reduce obstacles that often prevent people

from starting or continuing the Elimination Phase in the first place.

Those barriers can include cost, cultural food mismatch, the energy demands of

preparing every meal from scratch and the social isolation that can come

with a highly restrictive approach.

For many people, Modified AIP is the version that they can actually begin

and more importantly, stick with long enough to see meaningful change.

That is so important because the Elimination Phase only works if

you can stay engaged with it.

First, let's talk about accessibility and affordability.

One of the biggest advantages of Modified AIP is that this improves both.

By allowing foods like rice, most legumes and pseudo-grains,

Modified AIP makes it possible to rely on familiar budget friendly

staples that are widely available.

It also reduces the need for specialty ingredients, which can be expensive or

hard to find depending on where you live.

Meal planning often becomes simpler also.

Fewer restrictions, fewer substitutions and more flexibility

in how your meals come together.

This is so important because healing shouldn't be just reserved for

people with high resources, a lot of time, or really good access to food.

Modified AIP helps meet people where they actually are.

Now there are certain groups of people for whom Modified AIP is often the most

appropriate starting place, and I'm going to run through them right now.

First, let's talk about vegetarians.

Now, Core AIP is not appropriate for vegetarians or vegans.

It removes too many protein sources and is just not possible

to meet basic nutrient needs.

Now, I know there are people out there that do it.

I'm here as a nutritionist with a history of being vegan myself,

telling you, please do not do this.

There are not enough protein sources to meet minimum nutrient needs,

and you can definitely be setting yourself up for some problems.

Now, Modified AIP, on the other hand, can work very well for vegetarians, but

it does require intentional planning.

When we exclude animal foods or we limit them, nutrient density

becomes even more important.

So vegetarians following Modified AIP need to pay close attention to

getting enough protein intake, their iron levels, their B12 and zinc.

So this is definitely not a wing it and see what happens situation.

I really recommend planning, tracking, and sometimes professional support

that can be essential to ensuring that your nutritional needs are being met.

But it is absolutely possible with the Modified protocol.

Now Modified AIP is also a better fit for people who are highly active, training

regularly or working to restore weight.

This version provides easy sources of starchy carbohydrates, better

support for energy demands, training and recovery, and a sustainable

approach to weight restoration.

So for these populations, Core AIP can sometimes be too restrictive,

increasing that physiological stress rather than reducing it.

So in this case, Modified AIP allows the body to feel adequately fueled

while still honoring the principles of the elimination process and healing.

Now I want to talk honestly about the research because this is where a

lot of reasonable questions come up.

Core AIP has been studied and Modified AIP has not-- yet!

All of the published research on the Autoimmune Protocol to date

has used what we now call Core AIP.

This is where the clinical remission rates, the symptom improvements, the

inflammatory marker changes come from.

Modified AIP is newer and hasn't yet been studied as a distinct

intervention in clinical studies.

That being said, it's important to understand what

this does and does not mean.

In practice outcomes with Modified AIP have been very strong.

Practitioners, coaches, and people using AIP on their own have reported

meaningful improvements in symptoms, energy, digestion, and quality of life

when using this more flexible approach.

Of course, these are anecdotal reports, not controlled trials,

but they are still important.

What we don't yet have and what I very much hope we will have soon, is

head-to-head research comparing Core and Modified AIP in the same populations.

I can't wait to see that data.

And if you are a researcher interested in partnering with me to

make that happen, I am here for it.

This will absolutely help us better understand who benefits

most from each approach, whether outcomes differ meaningfully, and

how we can continue refining AIP to serve more people effectively.

And this is the key point I want to leave you with here.

The absence of research is not the same thing as absence of effectiveness.

It simply means the research hasn't been done yet.

Modified AIP exists because of what we've learned from real world use and

because we always want more data and better data, it's okay to use the best

information we have right now to make a thoughtful and individualized decision.

One of the most important differences between Core and Modified AIP isn't

about inflammation or effectiveness.

I actually think it's about nutrient density.

So Core AIP by design, it forces nutrient density.

Because more foods are excluded, you are naturally pushed towards meals built

around vegetables, high quality proteins, seafood and other deeply nourishing foods.

There are fewer convenient fillers, so nutrient-dense foods tend to take

up just more space on your plate.

Now with Modified AIP, that automatic push is just a little bit weaker.

The inclusion of foods like rice, beans and pseudo-grains can be

incredibly helpful for accessibility, affordability, energy, but they can

also crowd out those more nutrient dense foods if you're not paying attention.

So this doesn't mean that Modified AIP is less effective.

It means it requires more intention.

So I just wanted to bring this up.

No matter what version you choose, nutrient density is not optional.

It's foundational to healing, immune regulation and long-term progress.

And if you're following Modified AIP, the goal isn't to replace vegetables

and proteins with rice and beans.

It's to add those foods alongside an already nutrient dense foundation.

Think a plate still anchored by vegetables and protein with rice or legumes as a

supportive side, not the main event.

Seeds added for flavor and texture, not instead of whole foods.

Ghee used as a flavor variation.

And these ideas are especially important if you are vegetarian,

highly active, underweight, or managing multiple nutrient deficiencies.

In those cases, planning becomes even more important, not less.

Now, the Elimination Phase works best when it supplies your body with the raw

materials it needs to repair and regulate.

Food is information, but it's also fuel and both matter.

So whether you choose Core or Modified AIP, keep asking

yourself the same question.

Is this way of eating nourishing me or just meeting the rules?

Because the rules are not what's producing healing, the nourishment does.

At this point, some of you might be wondering if Modified AIP is the

starting point you recommend for most people then what happens to all of

those existing Core AIP resources?

The recipes, the meal plans, the cookbooks, the tools that so many

people have relied on over the years.

The answer is simple: they are still useful.

Modified AIP is not a replacement for Core AIP-- think of it as an additive approach.

Most Core AIP recipes and meals form an excellent foundation.

Even if you choose the Modified protocol, what you change is

how you build around them.

So, for example, you might take a Core AIP meal and then add a

side of rice, quinoa, or lentils.

You might sprinkle some seeds onto a salad or blend them into a dressing.

You might use ghee as a flavor switch up alongside your

olive oil or your coconut oil.

So the structure of your meal is really staying the same.

You've got your protein, your vegetables, your healthy fats.

You're just expanding it in thoughtful and sometimes more convenient ways.

And this is also why I wrote The New Autoimmune Protocol.

When Modified AIP was introduced, there wasn't a dedicated resource that showed

people how to actually cook this way, how to use those newly included foods

without drifting away from nutrient density or the Core principles of AIP.

So this book is the first AIP resource built specifically to include

Modified AIP recipes and the focus, again, not on relaxing the protocol.

It's on showing how to integrate foods like rice, beans, seeds, and

ghee intentionally while keeping meals vegetable forward, protein

centered, and deeply nourishing.

So if you already have Core AIP cookbooks or recipes that you love,

you don't need to abandon them.

Think of them as your base.

And if you're looking for guidance on how to cook for both Core and Modified

in a flexible, accessible, but still therapeutic way, that is where The

New Autoimmune Protocol fits in.

It bridges the gap between the original Core framework and the realities of how

most people live and eat now, and you can pre-order it wherever books are sold.

Before we wrap this up, I want to pause and talk about known

sensitivities because this is one place where some people get tripped up.

Whether you are following Core AIP or Modified AIP, there is

one rule that always comes first.

If you know a food doesn't work for you, you don't eat it.

No version of AIP overrides your lived experience.

Just because a food is included on Modified AIP doesn't mean

it's appropriate for everyone.

And the same is true for Core AIP foods too.

Even within the Elimination Phase, there are foods that some people

just don't tolerate well, dairy is a really common example here.

Even though ghee is included on Modified AIP, if you know that you react to

it or if you've had issues in the past, it's definitely not something

you need to push or test right now.

The same goes for legumes and seeds.

These foods work beautifully for a lot of people, but they can

still cause symptoms for others.

So if you have had a clear reaction or even a suspicion in the past, it's

definitely okay to leave them out.

Modified isn't about forcing those foods back in.

It's about creating a starting point that's flexible enough to adapt.

One more piece I want to name before we wrap up is cultural relevance, because

food is never just about nutrients.

Food is culture, it's family, it's memory, tradition, and identity.

And for a long time, one of the quiet barriers to AIP was that it didn't always

translate well across different cultures, food traditions, or lived experiences.

This is another place where Modified AIP can be so helpful by allowing

foods like rice, legumes, seeds, and certain traditional ingredients,

Modified AIP really opens that door to meals that feel a little more

familiar and connected while still honoring the principles of elimination.

So it might mean being able to adapt cultural dishes rather

than abandoning them entirely.

It might mean sharing more meals with your family easily, or it might mean

finally seeing yourself, reflected in the way you eat while you heal.

And beyond culture, this is also about making AIP your own.

Again, AIP is a framework, not a rule book.

Core and Modified AIP are starting points, not end points.

They're meant to be adapted based on your symptoms, your access

to food, your values, and the season of life that you are in.

You are absolutely allowed to adjust within that structure, learn as you go or

change your approach as your body changes.

The goal of the Elimination Phase isn't to follow a plan perfectly.

It's to gather information, build stability, and move

forward with more clarity.

When AIP fits into your life, rather than asking your life to completely

reorganize around it, that is when it becomes sustainable, and sustainability

is what allows healing to actually unfold.

One last thing I want to touch on is what do you do if you start with

Modified AIP and then you suspect that something still isn't working?

Starting with Modified doesn't lock you into that version, and it doesn't mean

that you have chosen the wrong path.

If you're following Modified and you notice that your symptoms aren't

shifting the way that you had hoped, your inflammation still feels kind of

high, or you suspect that one of those Modified inclusions might be getting

in the way, you already have a really useful next step available to you.

You can transition from Modified to Core, and the good news is that you

have already done most of the hard work.

You've learned the structure of the Elimination Phase.

You've built some new routines and you've adjusted your kitchen

and your shopping habits.

At that point, moving to Core AIP simply means removing those Modified

additions, the foods like rice, legumes, seeds, ghee, and pseudo-grains, and then

committing to a focused window of time.

I generally recommend trying this for at least three weeks.

That gives your body enough time to fully respond, inflammation to settle

and symptoms to show a clearer pattern.

Without it turning into this open-ended restriction where you're flip-flopping

from one elimination to the next.

It definitely does not need to feel like starting over.

Again, it's a structured experiment built on that work that you have

already done, and if you notice that meaningful improvement during those

three weeks, that's valuable information.

You can then decide whether you're going to continue Core AIP a bit

longer or move forward with a more intentional reintroduction process.

And if you don't notice a change, that's information too.

It may point you towards other factors that need attention beyond

food or some troubleshooting.

Either way, you're not going backwards, you are refining your approach.

Let's take a moment to pull everything together.

The Elimination Phase is a powerful tool, but it's just one phase of a

three phased process, and there's more than one way to approach it well.

Core AIP and Modified AIP share the same purpose: to calm, inflammation,

support, immune balance, and to help you learn how your body responds to food.

The difference isn't about commitment or discipline, it's about fit.

Core AIP is the most comprehensive version.

It can be incredibly effective in the right context, especially when

you have flexibility, support, and resources to fully engage with it.

Now, Modified AIP is designed to be accessible, affordable, and more

sustainable while still honoring that therapeutic foundation.

You already know it's the version I recommend most people start with today.

Neither approach is better, but one might be better for you right now.

Remember, the Elimination Phase is temporary.

What you're really building is understanding, confidence and

a foundation that you can carry forward into reintroduction

and long-term sustainability.

And if you want guidance for what AIP looks like today with recipes and

meals designed specifically around Modified AIP while still prioritizing

nutrient density and therapeutic principles, that is exactly why I

wrote The New Autoimmune Protocol.

It's the very first AIP resource created to reflect this updated, more flexible

approach, and it's designed to help you put all of this into practice in a

way that actually fits into your life.

You can pre-order The New Autoimmune Protocol now and you'll

find the link in the show notes.

Thank you guys so much for being here, for listening and for doing

this work with care and intention.

I will see you next time.