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What I Wish I Knew When I Started the Autoimmune Protocol (AIP)

Many autoimmune disease sufferers are starting the autoimmune protocol (AIP) in an effort to find wellness.

It makes my heart happy to hear others are starting the autoimmune protocol because it truly has been one of the keys for me in unlocking wellness!

With that said, starting the autoimmune protocol was one of the hardest things I’ve ever done. I can hardly believe it’s been almost a year since I started the elimination phase, and I now find myself in the reintroduction phase. 

While out on a walk the other morning, my thoughts turned to what I wish I had known when I started the autoimmune protocol (AIP), so I decided to open up and share.

“The Autoimmune Protocol is not a set of commandments you desperately follow, hoping for a cookie-cutter result.  It is a deliberate journey of healing wherein you blaze a unique trail.”

Mickey Trescott, NTP and Angie Alt, NTC, CHC, The Autoimmune Wellness Handbook

Focus on what to Include

The autoimmune protocol is an elimination diet, followed by a reintroduction phase. 

When I started the autoimmune protocol, I focused on my “What to Exclude” list.  It took time for me to realize that the foods I included were just as important as the foods I excluded.  I saw increased wellness as I incorporated a variety of foods on the “include” list; each food providing a variety of nutrients.

Plan Ahead, and Prepare

I learned the importance of planning ahead on the autoimmune protocol the hard way. 

There were a number of times I left my house, thinking I would run a quick errand and be back in time for my next meal, then found myself caught up, hungry, with no options for food. 

As a result, I encourage you to plan carefully, prepare accordingly, and always have AIP friendly foods or snacks with you.  Before you leave the house, think about how long you will be gone, if you might get caught up somewhere, and pack AIP friendly meals and snacks accordingly.

Let go of Expectations

When I started the autoimmune protocol, I read that most people stay on the elimination phase for 30-90 days before starting reintroductions.  Therefore, I determined I would fall into the “30 days” category. 

In actuality, I fell into the more uncommon “10-11 month” category.  Yes, I was in the elimination phase for 10-11 months. 

Being so set on “30-90 days,” I felt a wide range of negative emotions when I had failed reintroductions.  Looking back, I wish I adopted an open mind, with no expectations other than finding wellness.  Now that I am in the reintroduction phase, I have no limitations or timeline on reintroductions other than to take things slowly and to listen to my body.

Lean into the Difficulty

Beginning the autoimmune protocol was no joke.  It was hard.  I wish I had known how hard it would be, and planned on leaning into the difficulty and trusting the process.  I

In time, I learned to recognize that I can do difficult things, and to embrace the difficulty rather than fight it.  As an autoimmune protocol seasoned veteran, I now know personally the health benefits it offers.  Moreover, the health benefits I receive through the autoimmune protocol outweigh every difficult moment along the way.

Understand the Science

I started the autoimmune protocol knowing very little about autoimmune disease, and even less about the autoimmune protocol.  However, my grit and determination got me through the first few weeks, then I felt my resolve slipping. 

As I felt my will power crumbling, I stumbled upon Dr. Sarah Ballantyne’s AIP Lecture Series.  I was hesitant to spend the money, but I took the leap of faith.  As a result, the lecture series ending up being instrumental for both my husband and I in understanding the science behind autoimmune disease and the autoimmune protocol.

Armed with a better understanding of the science behind what was happening in my body, I continued to successfully adopt the autoimmune protocol template into my lifestyle.  Most importantly, it has been instrumental in my finding wellness.  If you are not in a position to sign up for her lecture series, Dr. Sarah Ballantyne’s books are incredible resources in understanding the science behind autoimmune disease and the autoimmune protocol. 


I started the autoimmune protocol with a single page printout in my hand of what foods to exclude, and a prayer in my heart.  Within months, I found there are actually a plethora of autoimmune protocol resources, including many free resources.  There are books you can buy, blogs you can read, and websites dedicated to autoimmune protocol friendly food.

Here are a few of my favorite autoimmune protocol online resources:

The Paleo Mom / Dr. Sarah Ballantyne

My favorite resource for all things autoimmune protocol (AIP).  I own many of Dr. Ballantyne’s books, and use them as reference guides.  Moreover, I regularly search her blog for articles on autoimmune disease and the autoimmune protocol.  Dr. Ballantyne also cohosts “The Paleo View” podcast with Stacy Toth.

Autoimmune Wellness / Mickey Trescott and Angie Alt

Another favorite autoimmune disease and autoimmune protocol resource!  I own and love their Autoimmune Wellness DIY guidebook.  Their website is full of free resources, uplifting content, and autoimmune protocol support.  Mickey and Angie offer many resources for empowered Do-It-Yourself healing.  Further, you can also find many inspiring success stories on their website!

Phoenix Helix / Eileen Laird

I recently found this resource.  I love and relate to Eileen’s quote on the homepage.  “To anyone whose autoimmune disease knocked them down so hard, they wondered if they would ever rise again.  Never underestimate your ability to rise.  We all have a phoenix within us.”  Eileen’s website is full of resources in the form of books, blog posts, podcasts, and autoimmune inspiration.

Shop AIP

Shop AIP offers hundreds of autoimmune protocol products!  Such a great resource for those who do not have a health foods store close by, or those in an autoimmune flare struggling to grocery shop.  In addition, I love that Shop AIP is committed to giving 5% back to autoimmune causes!

Paleo On the Go

Real, fresh from the farm, prepared and frozen autoimmune protocol meals delivered directly to you!  My favorites include the Turkey Pot Pie, the Beef Breakfast Empanada, Minestrone Soup, and the Carob Delight Slim Mint Cookies.  I place an order once every month or two to have AIP meals in my freezer for those unexpectedly crazy days. Likewise, I like to have Paleo On the Go AIP meals on hand for when my autoimmune symptoms sneak up on me. Use the promo code “Shanna” to receive 15% off your first order.


I continue to successfully navigated the autoimmune protocol.  Please know that I am here for you if you have any questions, concerns, or comments.  I can offer my real-life experience, and point you in the direction of helpful resources.


Beginning the autoimmune protocol can feel very isolating.  Looking around, it can seem like there is no one to relate to.  However, there is an incredible autoimmune protocol community online.  I find comfort as I read blogs and connect with others on social media.  Likewise, when I started my Instagram account (@wellnessunraveled) last year, I was overwhelmed by the support and love in the AIP community.

Looking to connect with others, but not sure how to find them?  One quick and easy way is to search hashtags like #aip, #totesaip, #autoimmuneprotocol, and so on.  I love seeing how others follow the autoimmune protocol. In addition, I love to see what they eat!

Some of my favorite Instagram resources for autoimmune protocol recipes are:

@unboundwellness, @autoimmunepaleo, @fedandfulfilled, @grazedandenthused

I am Here for You!

Please know I am cheering you on in your autoimmune protocol adventures!  To clarify, I say adventures because that is where the autoimmune protocol can take you!

To a place of wellness, where you can go from living a life filled with autoimmune symptoms to living a life of adventures, feeling well more often than not.  However, it will not be easy, friend.  In contrast, it will be hard. But, the autoimmune protocol helps autoimmune warriors get their lives back every day! 

You are next!  You got this, and I’ve got your back!

“By addressing all the likely food and lifestyle culprits en masse, the Paleo Approach becomes a very powerful means of managing autoimmune disease.  It is the most expedient way to remove all the controllable triggers of your autoimmune disease and heal your body.  And while jumping in with both feet may seem intimidating, it’s also the fastest way to feel better.”

Dr. Sarah Ballantyne, The Paleo Approach

Note:  this post may contain affiliate links.  This means that if you purchase through the link, I will earn a small commission at no extra cost to you.  I ONLY link to products I personally use and strongly believe in!

Comments (25)

I was diagnosed over 13 years ago w/MS. My husband left me & took our 3 children. In the last year I’ve reconnected w/1 child(now 21) 2 are still “strangers” to me.
I really need help w/making my Life better.
Is there a written down, step-by-step regime that I could follow? I am presently in no shape to interpret a daily diet; I feel I could follow something if it were all spelled out for me. Many thanks.

Hi Edwidge,

Thank you for your comment. I feel honored that you opened up to me and shared with me some of your journey with MS. My heart is with you, and I am more than happy to help. There are written down, step by step guides that you can follow. Here is a great place to start: If you follow that link, there are simple easy to print foods to include, and foods to exclude guides. It may feel overwhelming depending on where you are at, but please know you are not alone. If you feel inspired to start the autoimmune protocol in stages, I recommend taking things slower; one step at a time. In other words, first focus on cutting out gluten/ wheat products. Maybe next focus on cutting out dairy. And so on. Also, I highly recommend finding a naturopath or functional medicine doctor to work with who can help you identify and address any nutrient deficiencies, supplements needs, or gut healing recommendations. Wishing you lots of wellness, and success as you embark on this new chapter in your life! Sending you love, support, and positivity. Shanna

I loved how you said “You are next” in healing. It’s brought tears to my eyes. ❤️U'
Shanna | Wellness Unraveled

Hi Lynda, Thank you so much for sharing that with me. It truly means the world to me. Sending you lots of love, support, positivity, and healing vibes!

It made me cry too Lynda! To think there’s an answer to getting out of this hell was like grabbing onto a life preserver in the middle of the ocean!

We can do this, AIP, we can feel better and confident from our success while accepting some temporary fails.
On vacation with friends then family was a challenge and I had some foods reintroduced like oatmeal, brown rice, and ice cream and different cheeses like goat and cheddar. My arthritis increased afterwards which tells me to get back to cooking and feeling better at home♥️

Yes! We can accept temporary fails – no problem at all! None of us are perfect, and we are all simply trying our best. So glad to hear you are back home and on the road to feeling better. Thank you so much for opening up and sharing your experience Lynda!

Now I am fighting tears! Thank you for sharing Diane! SO beautifully said, and I relate!

Homeschooling mom dealing with 2 or 3 autoimmune diseases here… I want to be next!! I told my husband I am starting whole thirty but I think it needs to be AIP, he thinks it’s going to be thirty days, but I imagine I will be more like you; around a year or so… thanks for sharing your story.

Hi Marsha! Such an honor to meet a fellow homeschooling autoimmune warrior! You can be next! I am so excited for you. I’ve heard wonderful things about the whole 30, and I myself focus on eating whole, nutrient dense, clean foods. If you think about it, please keep me posted. I would love to hear how your AIP journey goes! Cheering you on sister! Hugs!

This is the first time I have visited your blog. Very encouraging! I am not familiar with your story, so I apologize if you have covered this question. Does your whole family follow the AIP with you? I have followed a yeast free diet a couple of times, and felt wonderful. I, too, am a busy homeschooling momma, and being a short order cook was not a great idea. I don’t have an autoimmune disease, but just did it for health. Now, my 10 year old daughter is having health issues, and this diet has been recommended. One of the reasons I did not include them on those diets was that I was concerned about them losing too much weight. My 10 year old is below her own growth curve. She’s also extremely picky. Do you have any advice for me? Thanks!

Hi Stacy, I am so sorry for the late reply! I was at my first NTP workshop weekend when you commented, and then our family moved right after. Thank you for your kind words! My whole family does not follow the AIP with me…well, they do and they don’t. Meaning, this is usually what my kids’ meals look like:
Breakfast – usually they eat a non AIP breakfast like eggs/bacon, paleo waffles, gluten free granola, etc.
Lunch – Usually eat an AIP lunch (whatever I make) and will sometimes add a side like homemade gluten free bread.
Dinner – Our whole family eats an AIP dinner (whatever I make) and I occasionally add a non AIP side for my husband and kids (rice, red potatoes, gluten free rolls, etc).
Usually once a week my husband or I make a non AIP meal for him and the kids for lunch or dinner like gluten free spaghetti…if I have AIP leftovers (but not enough leftovers for everyone).
So, most of the time our family eats AIP.
I met a friend at the Paleo Mom Workshop whose daughter (I think she’s around 5 years old) is on AIP for health reasons. Her daughter’s health improved on the AIP. Email me if you are interested in connecting with her, and I can connect you two. I am not a medical professional and cannot give medical advice, but from my perspective as a mama and an experienced AIPer, if I suspected AIP might help one of my kids, I would not hesitate to do it. I would make sure I macro-balance their meals and include plenty of healthy fats with their meals, and a variety of nutrient dense foods. Also, I’ve found that my kids’ pickiness in eating has improved since I’ve started AIP and expose them to more foods, and explain the health benefits of the foods. I try to relate it to them (this food helps with x,y,z so it will help you with …insert whatever your daughter loves to do). Also, I’ve found getting my kids involved in preparing meals and snacks encourages them to take responsibility of the meals, and be more willing to try new things. As a bonus, we spend quality time in the kitchen. Also, setting the example. Them seeing me change my eating habits for good made a difference in their eating habits. Let me know if you have any other questions. Sending you SO much love and support from my mama heart to yours!

Hello I am Melanie I have been sickly as long as I can remember. In 2016 I finally went to a rheumatologist who at that time diagnosed me with connective tissue disease. I had tested positive in 2015 for lupus and also found out I had the Mthfr gene. My rheumatologist didn’t diagnose me as lupus until 2017. I have been on plaqunil, methotrexate, benlysta, celcept, and one other medicines that I have forgotten because I probably only took it a few days or maybe a week. I hated being sick so I got with a kinesiologist. That talked to me about amp. I have been trying to figure it out mostly on my own as she told me I cold text her any time if I had ny questions well I have tried nd she I feel bad for asking her for help as she doesn’t text me back. Well I as just hoping I am not the only one who has back slider and ate bread and found out I have eaten things that aren’t aip approved. I guess I just need some support to know I/we all make mistakes.

Hi Melanie! It’s a pleasure to meet you! Starting the AIP can be difficult and confusing! There are SO many resources online, and free starter guides. I have a Back to Basics guide to the Autoimmune Protocol that you can get by clicking here:

Or if you are looking for more in depth / detailed information, these are GREAT resources: (Be sure to sign up their newsletter for a AIP Quick Start Guide)

Also, I recommend purchasing or checking out from the library “Autoimmune Wellness Handbook” by Mickey Trescott and Angie Alt, and “The Paleo Approach” by Sarah Ballantyne.

Sending you lots of love and support. It takes time to learn the AIP, but it REALLY is worth the effort! Hugs!

Thank you, thank you, thank you! I’m at the very beginning of my wellness journey having been just recently diagnosed with Graves’ disease. Reading here has made me feel so much more confident in the dietary changes I’m embarking upon and my perspective on elimination has shifted too. I’m so glad I stumbled upon your site!

You’re welcome Melissa! I’m so glad you found my site! I am so glad you found answers and have a diagnosis. Sending you SO much love and support as you start the autoimmune protocol…I am SO excited for you and the changes you will see. BIG hugs! And let me know if you need anything!

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