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What to Do When AIP Doesn’t Work

What to do when AIP doesn’t work is important to understand…

The autoimmune protocol (AIP) is an elimination diet that helps many autoimmune disease sufferers find relief from their autoimmune symptoms. Further, the autoimmune protocol provides lifestyle support for living well with autoimmune disease.

However, the AIP diet is not a one size fits all kind of diet.  Rather, it is a template for autoimmune disease sufferers to customize, fine tune, and adjust to fit their own unique nutritional and lifestyle needs.

While many autoimmune disease sufferers, including myself, find life changing relief from autoimmune symptoms, others may need to dig a little deeper if the AIP diet does not seem to be working.




Each of us are unique with our own unique set of circumstances, and nutritional needs.  As a result, it is important to find an individualized approach to the AIP diet that supports our own body.

Likewise, it is important to make adjustments, and add back in reintroduction phase foods, as our journey progresses.

Just as no two autoimmune diseases manifest in exactly the same ways, no two AIP journeys will look exactly the same.

When AIP Doesn’t Work:  Keep a Food and Mood Journal

If the AIP does not seem to be working, try keeping a food and mood journal for at least three to five days (the longer the better).  Record everything you put into your mouth, along with mood and energy levels.  Also track your water intake, your sleep patterns, any kind of movement, as well as your bowel movements and digestive reactions.

Look back at your food and mood journal, and start to identify patterns.  Some questions you may want to ask yourself when reviewing your food and mood journal: 

Are you getting in a variety of properly prepared, nutrient dense foods?

Do your energy levels dip after you eat certain foods?

Do you have a digestive reaction after eating certain foods? 

Do you feel better when you eat more healthy fats? 

Do you feel worse when you eat certain types of foods? 

Do you feel better or worse when eating starchy vegetables?

Are you not eating enough food? 

Do you feel best when you eat three larger meals or 4-6 smaller meals?

Are you are moving your body enough, and in supportive ways?

Are you having regular bowel movements on certain days but not others?

Is your sleep suffering?

Do you need to add more gut healing foods to your diet?

A food and lifestyle journal can be instrumental in helping you identify any issues your body may be having with AIP approved foods.  If you are working with a naturopath, nutritional therapy practitioner, or AIP coach, be sure to share your food and mood journal with them for additional insights.

Click here to download a FREE AIP food and lifestyle journal. You can print as many copies as you’d like!


When AIP Doesn’t Work:  Including a Variety of Properly Prepared Nutrient Dense Foods

Keeping track of all of the excluded foods on the AIP diet can feel overwhelming.  Further, it can be tempting to simply find one to three favorite AIP meals that you love and stick to those for the entire time you are on AIP.

However, one of the purposes of AIP is to flood the body with a variety of nutrients the body needs to repair and restore. 

If you are not feeling as well as you think you should be on AIP, revisit the foods you are eating, and be sure you are consuming a wide variety of nutrients. 

Some tips and tricks:

Make it a game with your kids.  See how many different colors of veggies you can eat in one day!

Revisit the “foods to include” list and pick some new veggies to try this week.

Try a different variety of vegetables than you usually buy.

Buy a new AIP cookbook, or look up some new AIP recipes.

Change up what kind of meats you use, and try to include some organ meat (you can hide it in a recipe).


“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.” 

Dr. Sarah Ballantyne, Paleo Principles


When AIP Doesn’t Work:  Macro-balance Your Meals

Are you eating a healthy balance of fat, protein, and carbohydrates (in the form of vegetables) appropriate for your own bio-individual needs and activity level?

Aim to include healthy fats, protein, and carbohydrates, in the form of vegetables, at every meal.

If you are struggling with energy levels, you can track your macronutrients using a free online tool, like cronometer, and make adjustments as necessary.

If you are working with a Nutritional Therapy Practitioner, or other nutritionist, they can help you determine your ideal macronutrient needs, and recommend adjustments based on your circumstances and activity levels.


When AIP Doesn’t Work:  Limit Natural Sugars

There are a number of AIP approved fruits and natural sugars.  However, just because a food is AIP approved does not mean it is fair game to eat all day every day!

There are many amazing recipes for AIP baked treats and sweets, along with some yummy AIP desserts available online.  If you are still struggling with your symptoms while on AIP, take a closer look at how many AIP treats and packaged snacks you are eating.  Try replacing your AIP sweets and packaged snacks with nutrient dense whole foods instead, and see how you feel.


When AIP Doesn’t Work:  Eating Enough Food

It can be a shock to the system to go from relying on higher calorie convenience food and possibly protein shakes to eating real, nutrient dense, whole foods.  More than likely, the quantity of food you will be eating on AIP is much higher than the quantity of food you ate prior to starting AIP. 

If you are struggling with low energy levels, consider if you are eating enough food.


When AIP Doesn’t Work:  Meal Spacing

Consider meal spacing based on your nutritional needs.  Do you feel best eating three larger meals per day, or four to six smaller meals per day? 

At the beginning of my AIP journey, I felt better eating multiple smaller meals a day.  As my journey progressed, I transitioned to three larger meals a day. 

Try to avoid skipping meals whenever possible.  If you have a busy day out and about, plan ahead and pack your AIP meals and water accordingly.


When AIP Doesn’t Work:  Consider Hydration

Are you drinking enough clean water?  Some symptoms of dehydration can actually mimic some autoimmune symptoms.


The rule of thumb I recommend is to aim to drink half your body weight in water each day.  If that feels overwhelming, simply try to drink one extra eight ounce cup of water each day, and work your way up from there.


When AIP Doesn’t Work:  Cut out Cheat Meals

If you are still feeling unwell on AIP, ask yourself if you’ve truly been on AIP 100% of the time since you started.  The 80/20 rule, where you eat healthy 80% of the time, then eat whatever you want 20% of the time is a popular rule, but it usually does not work when it comes to AIP.

Cutting out your weekly cheat meal may be the difference between feeling your best and struggling with symptoms.


When AIP Doesn’t Work:  Consider AIP Lifestyle Factors

As important as the nutrition side of the autoimmune protocol is, the lifestyle side of AIP is also incredibly important!

Some things to consider:

Are you sleeping enough?

How is your quality of sleep?

Are you chronically stressed?

Do you move your body enough?

Are you getting outside and spending some time in nature?

Are you connecting with your loved ones?

Are you working on reducing toxins in your environment?


When AIP Doesn’t Work:  Consider Cross Contamination

Are you eating out while on the AIP?  If so, consider whether cross contamination may be an issue.  Despite our best efforts when eating out, cross contamination can happen anywhere to any of us.


To decrease the risk of cross contamination, be sure to clearly communicate with your server, chef, and/or manager.  Hand them an AIP allergy card.  You can download a free AIP allergy card here.


Resource Highlight:  The Paleo Approach Chapter 8

If the AIP doesn’t seem to be working for you, and none of the above suggestions are resonating with you, I highly encourage you to get your hands on The Paleo Approach by Dr. Sarah Ballantyne.  Open it up to chapter 8, and dig in! 

Dr. Sarah shares many things to consider when troubleshooting the AIP, including:


Poor digestion.

Digestive supplements to consider including stomach acid, digestive enzymes, and probiotics.

SIBO – Small intestinal bacterial overgrowth.

Persistent infections and parasites.

The gut brain axis.

Allergies and sensitivities.

Eating seasonally and cycling foods.

Histamine intolerance.

Cross contamination.

Organ system support.

Tightening up blood sugar regulation.

Micronutrient deficiencies.

Healing and repairing your gut.

Modulating your immune system.

AIP lifestyle factors to consider.


If the AIP Diet Still Isn’t Working

If you’ve considered each of these things, please work with your medical team or Nutritional Therapy Practitioner to find another nutritional protocol to support your health, and get you to a place where you are living your best life!


If the AIP Diet Feels Hard…You are Not Alone

Starting, and living the autoimmune protocol can feel all kinds of difficult. 

In fact, it’s 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 customize the AIP to your unique needs, but finding relief from your autoimmune symptoms is possible!

I am cheering you on and 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!


Autoimmune Protocol (AIP) Books I Love


The Paleo Approach by Dr. Sarah Ballantyne

 The Autoimmune Protocol Ebook by Dr. Sarah Ballantyne

A Simple Guide to the Paleo Autoimmune Protocol by Eileen Laird

Reintroducing Foods on the Autoimmune Protocol by Eileen Laird

Autoimmune Wellness by Mickey Trescott and Angie Alt




Links I post may contain affiliate links, which means: any items purchased through the links I post, I will earn a small commission at no additional charge to you. Please know I only link products I personally LOVE!


Comments (2)

I started AIP about a week ago and I am sad to say that I don’t think it will work for me. I have ulcerative colitis and my system simply cannot handle the high amount of vegetables. I was avoiding harder to digest vegetables before the diet and after a week of following a program I feel worse than I did before I started. Cruciferous veggies are a complete no. Leafy greens hate me too. I decided to stick with the elimination of soy, gluten, and dairy but the truth is I have to be able to incorporate some gluten free pasta or rice or something else to fill in a meal with meat besides veggies 2-3 times a day. Have you heard of people having this problem before?

Shanna Nemrow

Hi Tessa! Thank you so much for reaching out. There are so many ins and outs when it comes to the autoimmune protocol, and there are so many ways to customize it and to make adjustments. I will say that suddenly eating a lot of veggies can be a huge change on the digestive system – and generally speaking, I do recommend increasing veggies slowly over the course of the first days / weeks of AIP to allow the body time to adjust. Everyone is different, and it’s so important to listen to your body. Bone broth and healing soups can be very helpful, generally speaking. Also, eating cooked veggies is generally easier on the digestive system than raw. Unfortunately, I cannot comment or give individualized advice / guidance unless I am working with a client one on one or in my group coaching program. If you’d like more info on either of those options, feel free to email me at I also have my next AIP online group coaching program starting March 15th if you are interested. You can go to for more info. ❤️ Also, just a reminder that the AIP is not just about food but also lifestyle – sleep, stress, movement, etc. 😉 Sending you so much love and support!

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