Troubleshooting the Autoimmune Protocol – A Guide

Troubleshooting is the process of looking for (and sometimes treating) those pesky underlying root causes as you undergo the healing process. While many people experience success straight out of the gate with the Autoimmune Protocol, others have complex issues that impede their progress. Today, we are going to talk about how to go about the troubleshooting process in a methodical way to avoid overwhelm.

When do you need to troubleshoot?

There are generally two reasons why you’d begin the troubleshooting process:

  • When you’ve done the recommended 30-90 days on the elimination diet and see no, or very little improvement (generally, I recommend those at the 30 day mark to give it more time instead of jumping in lieu of troubleshooting too soon).
  • When you continue to experience new symptoms past the initial adjustment period to the elimination diet.

When do you not need to troubleshoot?

You shouldn’t begin troubleshooting when you are transitioning to the elimination phase of the Autoimmune Protocol for the first time. It is easiest to see where you get with the dietary and lifestyle recommendations before diving in to exploring other potential changes. This is a really big mistake I see people making in our community, especially when it comes to those extra layers of restriction (low-FODMAP diets, etc.). Again, we are trying to avoid overwhelm here!

First steps to troubleshooting

So, you’ve decided you need to do some further exploration to determine what is standing in the way of deeper healing. Here are some of the first steps you can take:

  1. Determine which area of troubleshooting you want to explore first. It is best to work through these areas one at a time, to make sure you are giving them a thorough investigation, and to not put too much on your plate. You will find details about how to pinpoint this in the next section.
  2. Hire someone to help you. Many people undertake the Autoimmune Protocol on their own (although we always recommend clearing these changes with your doctor) to get at the root of their food sensitivities. Once you hit some of these troubleshooting issues, it is important to have a practitioner who can help guide you through the process and order any testing that may be needed. This type of help can range anywhere from a health coach to a doctor who is well versed in AIP and functional medicine (check out AIP Certified Coach for listings of practitioners we recommend).
  3. Get in the right mindset. Troubleshooting can often take time, and it is important to have patience with this process. Clarifying your goals, expectations, and process will help you avoid overwhelm with all of the possibilities out there.

Areas to explore

Moving on, let’s talk about the three main areas of exploration when embarking on the troubleshooting process. Below, I’ve given you a little overview of some situations where I’d consider a need for troubleshooting in each category.

#1 Diet: This would include any modifications to the diet in addition to the recommendations made on the Autoimmune Protocol, including additional supplementation if needed.

When to troubleshoot:  Those who experience continuing digestive difficulties (reflux, heartburn, indigestion, nausea, bloating, gas, abdominal pain, diarrhea, or constipation) on the elimination diet (either in general, or as a response to certain foods in the diet).

List of things to look into (preferably with the help of a practitioner):

  • Not eating enough carbohydrates
  • Not eating enough nutrient-dense foods (like organ meats and probiotic foods)
  • Not eating enough vegetables
  • Hydration
  • Blood sugar imbalance (hypo- or hyper-glycemia)
  • Low stomach acid
  • Enzyme deficiency
  • Bile deficiency/no gallbladder
  • Low levels of beneficial bacteria
  • Vitamin or mineral deficiency
  • Carbohydrate or starch intolerance
  • FODMAP intolerance
  • Fructose malabsorption
  • Additional food sensitivities
  • Histamine intolerance
  • Oxalate, sulfite, or salicylate sensitivity
  • Cross-contamination of gluten or other food sensitivities

It is important to note that some of these areas (most notably FODMAP and histamine intolerance) can indicate issues that may need to be treated, for instance SIBO (small intestine bacterial overgrowth) or methylation dysfunction, both of which will be discussed in the medical section.

Some of these items are easily remedied with your own observation and by making simple changes – such as the simple problem of feeling tired on AIP due to needing more carbohydrates. Others, like additional sensitivities or digestive difficulties might take some time, trial, error, and testing to chase down.

#2 Lifestyle: There are many areas you may not have explored when transitioning to the elimination diet, and for some people, these areas impact their health even more than food.

When to troubleshoot: Those who experience energy fluctuations, fatigue, chronic pain, trouble falling asleep, staying asleep, waking up too early, or poor quality sleep, anxiety, depression, mood fluctuations, weight loss resistance, or reduced ability to handle stress.

List of things to look into (preferably with the help of a practitioner):

  • HPA-axis dysfunction (otherwise known as adrenal fatigue)
  • Barriers to sleep
    • Bad habits (sleep/wake times, routines, blue light exposure)
    • Unmanaged pain
    • Dietary factors (blood sugar, caffeine, alcohol)
    • Underlying sleep conditions (sleep study may be helpful here)
  • Lack of stress management
  • Improper movement (too much or too little)
  • Lifestyle mismatch (eg. an extremely stressful job or shift work)

#3 Medical: These are areas that you need a doctor (either a traditional M.D. or D.O. or a natural N.D.) on board to help order testing and prescribe treatment if necessary.

When to troubleshoot: Those with any ongoing issues that have not resolved with dietary and lifestyle interventions, or even those that worsen with dietary changes.

List of things to look into (preferably with the help of a practitioner):

  • Gut infections
    • SIBO (small intestine bacterial overgrowth)
    • pylori
    • Bacterial overgrowths
    • Parasite infection
    • Fungal overgrowth
  • Methylation dysfunction (MTHFR and other genetic mutations)
  • Hormone imbalances
    • PCOS
    • Thyroid dysfunction
    • Estrogen dominance
  • Micronutrient deficiencies
  • Toxic exposures
    • Mold
    • Heavy metals
    • Environmental exposures (such as at home or work)
  • Chronic viruses/infections (like Lyme or Epstein-Barr)
  • Structural or physical conditions
  • Need for mental or emotional support

As you can see, troubleshooting can be quite an involved process and you can easily get overwhelmed. The good news is, that many people are able to reach a new level of healing after troubleshooting some of these root causes.

What my troubleshooting process looked like

I experienced slow progress with the Autoimmune Protocol, but I came into the elimination diet bedridden and incredibly sick (you can read more about my story here). At the 9-month mark I was feeling about a 75% improvement from where I started, which felt pretty incredible at the time, but I noticed that my progress had plateaued. No matter what I did, I seemed to be “stuck” at that amount of healing. After becoming increasingly frustrated with my own efforts to further restrict my diet (I tried a ketogenic approach, low-FODMAP, and low-histamine at various intervals), I hired a naturopathic doctor to troubleshoot with me, and we found a host of issues – a need for thyroid replacement hormone, gut infections (H. pylori and a parasite), and methylation issues, all of which needed treatment over the next year.

After treating these root causes (which took over a year), my healing process skyrocketed. I know for sure that I would not have been able to do the deep healing that got me back on my feet had it not been for that further testing and appropriate treatment for my specific issues. That being said, I am grateful the process happened when it did for me – I was able to see just how much diet and lifestyle had an effect on my body (a LOT!) and was able to hone in on those signs that there were still some issues that needed addressing.

A few notes on troubleshooting:

Sometimes troubleshooting includes receiving medical treatment for necessary issues. There seems to be a feeling in the community that those who have not healed without medication have failed, and we are here to tell you that that could not be further from the truth! If you are interested in learning more about the role of medication on the healing journey, check out Eileen Laird’s article Starting Medication after Four Years on the Paleo Autoimmune Protocol and if you’d like to hear about our very own Angie Alt’s take on surgery, check out Surgery the AIP Way.

Supplementation can often be a part of troubleshooting. I think it is best to work with a practitioner who is both knowledgeable about the use of supplements especially as they apply to the Autoimmune Protocol (check out the AIP Certified Coaches!), but there are some things you can consider if you are supplementing on your own. Check out the articles Supplements on the Autoimmune Protocol and Hidden Gluten, Grains, and Nightshades in Meds and Supplements on this site to learn more about supplementation.

I hope this article has given you some starting points as you begin your own troubleshooting process!

About Mickey Trescott

Mickey Trescott is a cook and one of the bloggers behind Autoimmune Wellness. After recovering from her own struggle with both Celiac and Hashimoto’s disease, adrenal fatigue, and multiple vitamin deficiencies, Mickey started to write about her experience to share with others and help them realize they are not alone in their struggles. She is a certified Nutritional Therapy Practitioner by the Nutritional Therapy Association, and is the author of The Autoimmune Paleo Cookbook, a guide and recipe book for the autoimmune protocol, and AIP Batch Cook, a video-based batch cooking program. You also can find her on Instagram.

15 comments

  • Annie says

    I have been doing the AIP elimination phase for approx 6 weeks. I have hashimotos and allopecia. Quite frankly it’s hard for me to determine how I feel on the hashimotos side of things but as far as the allopecia I can not get it under control at all. It’s been going on for 3 years but the last 5 months there has been drastic hair loss. To say I am discouraged would be an drastic understatement. Is there a list of drs I can look at? Am I at that point? I have been to quite a few and eventually they all pass me off. I live south of Seattle. Any advise is appreciated.

    • Mickey Trescott says

      Hey Annie! I am so sorry to hear. Unfortunately the doc I worked with when I lived in Seattle has since retired. I would search listings at the Institute for Functional Medicine, Re-Find Health, and Paleo Physicians Network for some leads. I hope you find some answers soon!

  • Bailey says

    Thanks for writing this article it’s given me a lot to think about. I’ve followed the AIP for up to 6 months at a time and haven’t seen much progress. Currently I’m just excluding nightshades, gluten, dairy, soy and legumes (which is still a LOT of things to eliminate and still live a normal life). I’ve also worked with a number of naturopaths (in New Zealand) who haven’t been able to help me at all. And i’ve spent THOUSANDS of dollars in the process. Most of the progress I’ve had has been by researching and following advice from learned autoimmune sufferers such as yourselves and Dr Ballantyne. I wonder if you can help me understand if there are ways that I can test myself for parasites and mold, or if there are tests that my GP can order and I can interpret the results myself? I think the quality of practitioner in New Zealand is very poor when it comes to helping people with complex autoimmune disorders and I feel like I have to take matters into my own hands.

    • Mickey Trescott says

      Hey Bailey! Unfortunately the tests I am aware of are here in the states. What you are looking for is a comprehensive stool test that looks for bacteria, fungus, and parasites. I might contact some functional medicine practitioners in NZ and ask what labs they use for stool testing. Then contact those labs and see if they will let you order direct from them. Or, you could hire a practitioner to help you (which you will likely need if you come back with any positives). Good luck as you navigate this step in your journey!

  • erica says

    I love
    reading all the information you give.I wish you would talk about microscopic colitis.There are very few websites that offer information on this autoimmune disease.
    Thank you

    • Mickey Trescott says

      Hi Erica! We try to cover the bases here, but with over 100 autoimmune diseases it is hard to address them all specifically. What we have found is that even though there are many autoimmune diseases, a lot of people find success using the same dietary and lifestyle interventions. Wishing you luck!

  • Alison Beere says

    Thanks Mickey, this is exactly the sort of insight I needed right now . Just started trouble shooting 🌻

  • Alexandra says

    Thanks for this piece. I was confused about one part though: “This is a really big mistake I see people making in our community, especially when it comes to those extra layers of restriction (low-FODMAP diets, etc.). Again, we are trying to avoid overwhelm here!” Are you saying not to do too many elimination diets at once? Thanks again 🙂

    • Mickey Trescott says

      Hi Alexandra! Yes, I am talking about adding in additional layers over top of AIP.

  • Pauline says

    Thank you for this helpful article Mickey. My dietary changes have been very helpful but I have also found that I have methylation disfunction. Having read your article I realise that this will take more time. I appreciated hearing about your own journey and the challenges that you needed to overcome. I am so glad that I found your book and podcasts. They have been both helpful and inspiring – thank you so much.

    • Mickey Trescott says

      Thanks for the kind words Pauline – wishing you luck!

  • C says

    I found that when i reintroduced eggs i actually felt better. Cheese too, particularly ones with traditional crusts. Although i think it’s a good exercise to eliminate and see how you feel, sometimes reintroductions can actually make you feel better too!

    • Angie Alt says

      That’s awesome C!

    • Mickey Trescott says

      C,
      100% agree, especially when those foods are nutrient-dense, like high quality eggs and cheese!

Leave a Comment