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:
- 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.
- 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).
- 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!
48 comments
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.
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!
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.
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!
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
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!
Thanks Mickey, this is exactly the sort of insight I needed right now . Just started trouble shooting 🌻
Happy you find it helpful Alison!
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 🙂
Hi Alexandra! Yes, I am talking about adding in additional layers over top of AIP.
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.
Thanks for the kind words Pauline – wishing you luck!
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!
That’s awesome C!
C,
100% agree, especially when those foods are nutrient-dense, like high quality eggs and cheese!
I am on AIP elimination (towards the end, approaching reintroductions first phase) and have had nothing but diarrhea since starting. Meals are balanced, I am taking enzymes, it is really frustrating. I thought eliminating dairy would rid me of my occasional constipation and loose stool issues but this is worse than I have ever been with regards to BM. I know enzymes are recommended for the increase in fat and animal meat etc. and I have been consistently doing that but not seeing it make any difference.
Miss G – Have you considered working with an AIP Certified Coach to figure out what might be best for you? -> https://aipcertified.com/coach-directory
Did you find an answer to this issue? It sounds exactly the same as what I’m experiencing at the moment.
I have some really clear FODMAP triggers: onions, cauliflower, inulin/chicory, coconut flour. I would like to try AIP (I have Pernicious Anemia), but I am terrified of the Diarrhea and painful bloating I get from those foods. Should I really try to incorporate them into my diet while on AIP elimination? My last SIBO test came back negative and my IBS symptoms are kept pretty well at bay through a mostly low-FODMAP diet.
Sarah, it’s possible to combine AIP & Low-FODMAP, but it is pretty restrictive & you have to work very hard to make sure you are getting enough carbohydrate. If you are getting negative SIBO tests now, I would first work w/ your doctor to slowly start working on reintroducing FODMAPs into your diet, determining which you tolerate & in what quantities. Once you’ve been able to expand your diet more, you could give AIP a shot & it will be less restrictive.
Hi Sarah! If you know those foods cause issues for you, I would recommend eliminating them while on AIP. A lot of people do the protocol with additional sensitivities – no reason to cause yourself distress when you are trying to heal! Hope it helps and wishing you luck.
Thanks for the replies! I am re-testing onion tonight. Fingers crossed!
How long is the initial adjustment period to the diet? Today is my 8th day on AIP and I’ve been experiencing a worsening of symptoms since I started. My stomach hurts more than usual and I’m having pretty frequent diarrhea. I’m wondering how long I should stick with it before I start troubleshooting. Thanks!!
Hi Michael! I’m sorry to hear you aren’t doing well, those symptoms aren’t typical with an adjustment to AIP. Is there anything you are eating a lot more of now compared to your previous diet – like certain vegetables or fats? Sometimes if people transition too quickly to a veggie and natural-fat loaded diet it takes their system a while to adjust. You could try backing off and doing a slower transition to AIP in order to give your body more time to adjust, or you could reach out to an AIP Certified Coach who can help you figure out the source of the issue and make recommendations. We have a directory of trained coaches here: https://aipcertified.com. Hope you figure it out soon! -M
Dear Mickey,
thanks for the helpful tipps, your website has been a major resource for my AIP journey.
I am histamine intolerant and AIP is a huge success for me. Basically, all my symptoms are gone, even some (like the incredible, constant fatigue) I didn’t even notice they were there.
My “trouble” with AIP, which is one not mentioned in the post, is that it actually even accentuated my weight problems. I started on AIP scratching on the lower end of a BMI of 18 due to my digestive symptoms.
Though I’m now going to the toilet just once a day, not 10 times like before, and even though I eat 3 big meals a day, I just can’t seem to put on any weight and my muscles are fading. A typical meal consists of lots of veggies + some starchy thing like sweet potato, plantain, maniok + some animal protein, and I do make bone broth and eat organ meats.
I’m quite an active person but now see myself struggling with my daily bike to work routine, while being in a better mindspace (alertness, concentration, cognitive performance, mood stability) than ever. I do plead guilty to a high pressure job, in public health, ironically. I have been on strict AIP for a bit more than 3 months now and am planning reintroductions. My symptoms were greatly improved after just a few weeks and entirely gone after a month and a half (the time some rashes take to heal), but I decided to stay on longer in order to give my body the chance to “forget” about some of the allergic reactions, which can take several months and I feel that my overall physical and mental condition still greatly benefits from it.
Any ideas for what I could do to gain some calories, given that reintroductions may also take several months?
Thank you so much!
Hi Karen! Thanks for the comment, and sorry to hear you are having trouble maintaining your weight on AIP! Here is an article you might find helpful: https://autoimmunewellness.com/overweight-underweight-weight-struggles-on-the-aip/
I would say if you continue to have persistent trouble in this area, seeking out the help of an AIP Certified Coach to look at your diet and see if you can make some reintroductions/modifications to help with this issue would be a good idea. You can find a listing here: http://aipcertified.com.
Thanks for your answer and the link to the article, which was helpful!
I will try the shake approach… and adding an AIP version of the “bulletproof coffee” (for the oil) to my breakfast which seems to be the “calory weak point” in my day.
I hope to report back in a few weeks so maybe the feedback can be useful for others 🙂
thanks again for your helpful website, it’s a huge resource!
Karen
I started the AIP protocol from a fairly “healthy” place (9+ years of low carb/paleo eating), lots of movement throughout the day, lots of outside time. I have Addison’s disease (adrenal), and Hashimotos. My biggest issue is aches and pains and I was starting to have some joint pain and swelling. Sleep hasn’t been great (fall asleep easily, but wake in the night). Started AIP in February b/c of the joint pain in my hands. Saw a bit of improvement in that, but about a month in I realized that my body aches and pains were gone (however, I was on double my hydrocortisone – steroid – dose than usual b/c the covid-19 outbreak had just started here and my stress levels went through the roof). Started adding things back in at the end of April, and the aches and pains came back so went back to strict AIP. It’s been almost another month and absolutely no resolution of symptoms (but I am back to my normal dose of steroids as well). At this point I’m not sure whether the reduction in the aches and pains was due to the high steroid dose or the diet. I eat meat, veggies, liver, homemade saurkraut, bone broth daily. Can’t see anything I’m really missing diet wise. Lots of outside time, walk 12+km/day. Very little sitting/sedentary time. Sleep has been a little better lately with the help of daily meditation that I started last month.
Just not sure how much longer I should be so restrictive with my diet, or just accept that the aches and pains might just be due to the low cortisol, and there isn’t a lot that can be done about it… Any thoughts?
Hi Heather! That sounds like a tricky situation. Unfortunately we can’t advise on situations involving medicine as we aren’t medical providers here. My suggestion would be to seek out a coach (we have a directory of folks we’ve trained here: http://aipcertified.com) to find someone who can take your history and help guide you. One thing to know is that not everyone feels their best without medication, and a lot of folks (including myself) use a combination of diet/lifestyle and conventional medication to feel symptom-free. Hope it helps!
No, sorry, wasn’t asking about medication, rather at what point do you decide that AIP isn’t doing what you had hoped. My autoimmune conditions are under control. Started AIP because of some joint pain and swelling, and also had a lot of body aches and pains. About a month in I noticed a reduction in the body aches and pains (no improvement on the joints though). However, I was also on a higher steroid dose at the time. Started to reintroduce a few things and the aches and pains came back (but also reduced my steroids at the same time). Went back to strict AIP and it has been another month and the aches and pains are as bad as ever. Not sure how much longer I should continue down the AIP path before deciding that food is not the issue?
Hey Heather, your question is too specific for me to answer without knowing all of the details. It could be that the steroids were taking care of the aches and pains, but also it could have been another factor (like less stress, sleep routine, etc.). It sounds like you need to do some more experimenting to figure it out. Dr. Terry Wahls is a great resource on combining DIY diet and lifestyle measures with medication – while this guidance doesn’t apply as well to steroids, she usually recommends her patients find a relief from symptoms for 6 full months using a combination of diet/lifestyle and medication before considering weaning them off, if medically possible (this is always a conversation you need to have with your prescribing physician, not DIY). Hope that helps!
I was very discouraged when I was well in the reintroduction phase of AIP to have my practitioner do an Alletess food sensitivities test which showed I am now sensitive to 26 out of 96 foods! I worked really hard in following AIP with reintroductions for over a year and would have thought that would have gotten rid of leaky gut, but it didn’t. I am worse off than when I started as far as reacting to all sorts of foods including a lot of healthy vegetables. I am now on an elimination diet but it is very restrictive due to all of the sensitivities I have. Any suggestions?
Hey Stephanie! I’m sorry to hear about your experience! In general, I find food sensitivity testing to be pretty all over the place and it doesn’t replace the hard work of trial-and-error through elimination and reintroduction. Personally I recommend folks skip the testing as it usually creates confusion and a more restricted process. Hoping for some smart guidance on the next step forward!
I wish it wasn’t so, but unfortunately AIP just hasn’t had a significant impact on my symptoms. I did the SAD to AIP group and have now been in the elimination phase for about 5 months. I’ve been working with an AIP certified coach and taking a bunch of supplements to support my adrenals and address bad gut bacteria and yeast overgrowth. I guess I wanted to reach out to say, at this point I am so emotionally and mentally done with being so restrictive when I’ve seen little to no benefit from it. I would like to start reintroducing, but its definitely hard to do when you’re not feeling amazing. Do you have suggestions/wisdom for people who need to reintroduce for their mental health, even though they continue to have symptoms. I am working on this with my coach, but it would be great to get even more support/ideas. Thanks!
Hey Elizabeth! I’m sorry to hear your progress isn’t living up to your hopes – and I’m happy you have a skilled coach to guide you through troubleshooting as it is so tricky to do on your own. First, yes, it is important to start expanding the diet if you are both burnt out on compliance and/or troubleshooting, and are starting to have some negative mental health effects. Not knowing your specific situation I can’t advise, but maybe you can take a “step back” that seems comfortable for you to maintain that still gets some of the major inflammatory culprits out (like gluten, dairy, nightshades, etc.). Also, it is worth mentioning that it might be time to look into combining conventional & DIY approaches (like diet and lifestyle) if you haven’t already. You didn’t mention your condition, but many folks find that the combination of a medication (like personally, I can’t thrive without my thyroid prescription) or might need another intervention to make a breakthrough. Wishing you luck Elizabeth!
Getting diagnosed with PTSD has been a big step. Most of my flare-ups seem to be stress related, but I spent a long time confused about what I was eating that made me feel bad. .. Little column A, Little column B? Probably.
Amy, stress can be a massive trigger for some people. I find that now that my diet is pretty dialed in, that most of my flares come from stress. I hope you find some practices that help you move the needle there for the long-term!
Hello!
I went on the GAPS diet solo three years ago. I felt amazing the first three months but after six months I had dropped an entire clothing size and began to lose muscle. My husband and I were worried about my health so I just went back to the way I had always eaten, with the exception of gluten free grains. My joint pain came back almost immediately as did my brain fog, but I just didn’t have the will power to go on such a strict diet again.
Fast forward 2 1/2 years. I began to have outbreaks of ulcers in my mouth for two weeks straight causing me to wake in the middle of the night with panic attacks. Because of that, I had to have my braces removed early. Things seemed to calm down a little until I sprayed my car with Lysol and began to have some sort of allergic reaction to the spray. Then I began reacting to food I had previously been able to eat. After ridding my home of every toxic cleaner and implementing only organic food, I am still reacting and having a hard time finding a Doctor who will not only LISTEN to me but who will WORK with me. I am currently on armor for my thyroid. I was diagnosed with IBS and I suspect I have Hashimoto’s as well. my body is a mess. I’m not sure where to start. Any suggestions?
Hey Sheri! I am so sorry to hear of your increasing sensitivity to environmental inputs and foods, that is really tricky to navigate! I think you are on the right track trying to find a practitioner that can listen to your story and help navigate the troubleshooting process. We’ve got a really great directory of coaches from all over the natural and conventional healthcare spectrum listed here, I would definitely look into finding someone who can help! http://aipcertified.com/coaches-directory
Great article thank you! Have Hashimoto’s and put myself on AIP about 3 weeks ago now and after 2 years a constipation things are perfect there! My sleep is also incredibly improved I’ve only had one sleepless night in 3 weeks. The problem I’m having is that I find myself feeling jittery, anxious, wound up within about an hour of waking up and sometimes palpitations during the day. I considered it might be my blood sugar but if it is I’m not sure what to do about it. I also find sometimes I’m light-headed and I wasn’t before this diet.
Hi Elizabeth! Those are some great wins in the motility and sleep department! The morning anxiety and light headedness definitely need attention though. Unfortunately we can’t do coaching over comments, but some things I would think about are if you are getting enough protein and fat often enough to stabilize blood sugar throughout the day, and if you are getting enough carbs in general to keep from feeling lightheaded. If you are looking for a coach to help you troubleshoot, we have lots of certified coaches here: http://aipcertified.com and if the symptoms persist, definitely check in with your medical provider.
Hey Mickey .thanks for the great article. I eat only low starchy veggies and some meat.If I eat any thing except that I determine severe seb. dermatitis and rash. So I avoided all fruits,starchy veggies,canned foods,glutine,processed foods.From a month a go I determined IBS .I want your sugestions plz, thanks Mickey .
Hi Mohamed! I’m sorry to hear that – unfortunately I can’t offer any coaching to people who are not clients. I would recommend finding an AIP Certified Coach who can take your history and make some recommendations. You can find a full listing here: http://aipcertified.com/coach-directory/
Hi Mickey,
thank you very much for your article. I am having a histamine intolerance and leaky gut syndrome. Currently on an elimination low-histamine diet for a month. Now I am thinking about starting AIP but it will be very tricky as in AIP many foods contain a high histamin. Do you have any suggestion please how to proceed with this so I won ´t get in a low nutritional state?
Many thanks
Kornelia
Hi Kornelia! I’ve written more about navigating histamine intolerance here: https://autoimmunewellness.com/could-histamine-intolerance-be-impacting-your-autoimmune-healing/
Hello! You mentioned a list of your recommended AIP coaches – are you able to share that, or know if anyone specifically in the Orlando, Florida area? Thank you so much!
Or an online coach is also a possibility – whichever you think is better! I’m 25 years old and am on AIP diet but not noticing a difference. I’m wondering about further restricting/testing for SIBO etc.
Hi Esther! We have many coaches in Orlando – check the directory here: http://directory.aipcertified.com. Good luck!