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Troubleshooting the Autoimmune Protocol (AIP)

Autoimmune Protocol (AIP) Meal of fresh fish and greens

Starting the autoimmune protocol (AIP) is rarely all rainbows and butterflies.  In my experience, it involves continual tweaking and fine tuning.  Even as I felt relief from many of my autoimmune symptoms, I noticed times when I felt better than others.  I learned to pay close attention to my autoimmune protocol eating habits, and to similarly monitor how I was feeling.  Troubleshooting the autoimmune protocol was key for my continued autoimmune wellness and success.

I truly believe in bio individuality, and that the autoimmune protocol is not one size fits all.  What works for me and my body may be a bit different than what works for you and your body.  Here I open up and share some of the ways I found relief from autoimmune symptoms by troubleshooting the autoimmune protocol, and share some resources to help you on your journey.

Getting a Variety of Nutrients

It can be tempting to find an AIP meal that you love, that is easy to prepare, and to eat it day in and day out.  I get it.  I’ve been there.  I am looking at you AIP tacos with homemade cassava tortillas!  However, it really is important to be sure to eat a variety of vegetables, healthy fats, quality proteins, and fruit.  In her book Paleo Principles, Dr. Sarah Ballantyne explains, “The immune system (and indeed every system in the body) requires an array of vitamins, minerals, antioxidants, essential fatty acids, and amino acids to function normally.  Micronutrient deficiencies and imbalances are key players in the development and progression of autoimmune disease.”

Limiting Natural Sugars

Just because a food is AIP approved does not mean it is fair game to eat all day every day.  A food I wish I could get away with eating all day every day? Fruit. I love fruit.  All kinds.  However, there were times when I noticed I felt unwell, and I could think back to eating too much fruit in one day.

Two of my main culprits during the warmer months (which is almost year round here in Southern California) are smoothies and pitaya bowls.  Not only are smoothies and pitaya bowls often filled with multiple servings of fruit, they also have coconut water in them which is high in natural sugar.  Yes, I still eat smoothies and pitaya bowls here and there, but I am careful to limit other fruit that day, and I am careful to pair them with a protein.

Including Protein in Meals

Learning the hard way, I discovered that if I eat a meal or snack without a protein source, I feel worse.  As I mentioned earlier, I currently eat three meals a day, with a protein at each meal.  If I eat a snack, I try to include protein as well.  Epic bars are my go to when I am on the go, or busy.  My favorite flavor is Bison.

Eating Enough Real, Whole Foods

When I started the autoimmune protocol, I went from drinking protein shakes multiple times a day, and eating gluten free breads, and other convenience foods to eating real, whole, unprocessed food.  To say it was a shock to the system emotionally and physically is an understatement.  Within days, I discovered that I needed to eat a larger quantity of food than I previously ate in order to keep my energy levels up.  Further, I learned to listen to my body for hunger cues, rather than depending on my mind to tell me how much food I should eat. Increasing the quantity of food I ate worked like a charm, and I found myself satisfied.

Meal Spacing

When starting the autoimmune protocol, I ate five to six smaller meals a day. I made this decision contrary to my reading that it was theoretically better for the digestive system to eat three larger meals a day.  At the time, I noticed that my body simply felt better eating multiple smaller meals a day.  Similarly, when I would try to eat three larger meals a day, I would not feel as well. As a result, for months, I listened to my body and did what felt best, which was eating five smaller meals a day.

Fast forward several months to today, I now eat three larger meals per day.  I cannot tell you when I made the transition; it just happened naturally as I listened to my body.  Now, thinking about eating five smaller meals a day makes my stomach turn, whereas the opposite used to be true.

Note: when I say “listen to your body,” I do not mean give into cravings! If your body is telling you to eat junk food, do not listen to it yet. It cannot be trusted. In time, as you continue to eat clean, your body will give you trustworthy clues as to what it needs. I promise it will never “need” sugary processed junk food, despite how strong a craving is.

Food Sensitivities

After a few months on the autoimmune protocol, I noticed that I felt a bit unwell at certain times.  I tried to identify a correlation to the foods I ate and the way I felt.  My findings?  My body had a sensitivity to onions, avocado, and garlic.  Three of my favorite foods that I ate a lot of everyday.

I knew I needed to eliminate them from my diet for a period of time.  It may sounds drastic, but I felt like I was starting the autoimmune protocol all over again when I eliminated those foods.  Sure enough, I felt better once I did.  In time (after a few months), I added onions, avocado, and garlic back in to my diet.  I find I do well with them as long as I limit how much I eat, and spread out the frequency with which I eat them.

Note: Onions, avocado, and garlic are all FODMAP-dense foods. While I did show some FODMAP sensitivity during a point in time, I seemed to have no reaction to other high FODMAP foods. If you are still experiencing symptoms on the autoimmune protocol, I encourage you to look into a low FODMAP diet, which can be combined with the autoimmune protocol.

“Fortunately, FODMAP intolerance will most likely disappear for most people as their guts heal and their gut microflora levels and diversity normalize.”

Dr. Sarah Ballantyne, The Paleo Approach, p. 212

Rushing Reintroductions

Oh boy, was I guilty of this!  Convinced I was only going to be on the autoimmune protocol for 30-90 days, I rushed reintroductions.  Not only did I rush them, I totally botched them.  Thinking I was invincible after my newfound wellness, I was sure I was ready for eggs, almond flour, and more all at the same time.  Nope, wrong.  My symptoms flared faster than I thought possible.  I found myself at what felt like back to square one.

Reverting back to the elimination phase, and filled with frustration, I gradually learned to think of the autoimmune protocol as a lifestyle change instead of a temporary elimination diet.  Almost a year after starting the autoimmune protocol, I am in the reintroduction phase, which is slow going because I keep forgetting to reintroduce new foods!  I am happy where I am, with the wellness I feel, and I feel fulfilled.  So I keep simply forgetting.  One of my new goals is to keep progressing with reintroductions by writing reminders on my planner to reintroduce a new food every two weeks.

“We know it’s tempting to start eating all of the foods you have eliminated right away after experiencing success, but embarking on the reintroduction phase carefully ensures that you don’t have to start over!”

Mickey Trescott, NTP and Angie Alt, NTC, CHC, The Autoimmune Wellness Handbook, p. 77

AIP Baking & Sweets

Confession:  when I started the autoimmune protocol, I had no idea there were ways to bake AIP style! Not a clue.  Therefore, I stuck to proteins, vegetables, fruit, and healthy fats.  I kept things simple.  I did not eat desserts for months.  Instead, I ate fruit for “dessert.”  Looking back, I am grateful I was clueless as to the wide world of AIP baking.  I often wonder if I saw such incredible improvement in my autoimmune symptoms because I kept things simple.

To this day, I choose not to bake AIP style.  Instead, when I would like a dessert or treat for the holidays or a birthday, I order something from Paleo On the Go.  In the past year, I’ve only ordered three AIP desserts from there.  I do not eat dessert very often.  The truth is, my taste buds changed and I no longer crave desserts.

I share my lack of AIP dessert experience with you to let you know I have very little experience with the link between AIP baking and desserts with feeling well on the autoimmune protocol.  Common sense tells me that too many baked AIP sweets impacts autoimmune wellness, but that limited quantities are okay.

Coconut, Plantain, & Cassava Chips

What I do have plenty of experience eating?  Coconut, plantain, and cassava chips!  I love them all!  With that said, I do not eat them very often.  I purchase a bag maybe once every month, and enjoy them over the course of a few days.  I do notice a difference in how I feel if I eat too many of them, which I learned the hard way, of course!


Some of my favorite resources for digging deeper into the autoimmune protocol are:

Dr. Sarah Ballantyne – her books, her website, and her AIP Lecture Series.  In her book, The Paleo Approach, Dr. Ballantyne dedicates an entire chapter on “When to Start Troubleshooting.”  She goes over poor digestion, supplements, probiotics, SIBO, infections, parasites, allergies, and much more.  If you are not seeing the results you hope for after a period of time on the autoimmune protocol, I encourage you to read Chapter 8 from The Paleo Approach.

Autoimmune Wellness – website and the DIY guide to living with chronic illness.

Well Wishes

Starting, and living the autoimmune protocol is difficult.  It is one of the hardest things I’ve ever done.  If you are struggling with the autoimmune protocol, please know you are not alone.  Give yourself some major props for your efforts, dedication, and grit!  Know you CAN do this, and that you can find wellness!  You may need to troubleshoot, but finding relief from your autoimmune symptoms is possible.  I am cheering you on and I am rooting for you!  Please let me know if you need anything at all.  I am here for you.  You’ve got this!  And I’ve got your back!

Other posts you may enjoy:

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

Autoimmune Protocol (AIP) Meal Planning

My Nutrition Journey…So Far (written 6-7 months into my AIP journey))

My Nutrition (AIP) Journey…Q&A (written 11 months into my AIP journey)

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