Finding the Missing Link: Troubleshooting on the Autoimmune Protocol

Why am I Still Not Feeling Better? Troubleshooting on AIP

Even after years of research, trial and error, doctors appointments and tests I still find that a small part of me wants to believe in the concept of a magic bullet; a simple answer, a single diagnosis, an “easy” fix. Honestly, this is a bit comical because every logical and educated part of me knows that no such thing exists. Our bodies are designed through an array of complex systems that all work together, or in some cases, fail together. When one piece of the system stops working every subsequent piece is thrown off and struggles to function properly. Having an autoimmune disease is the health equivalent of taking a beautiful and intricate puzzle and scrambling the pieces.

I spent about eight years living with my pieces scrambled. I had no diagnosis, no solution, I was just sick. I would go to the doctor and get testing done and try to see if we could find two or more pieces that fit together, but they never really fit. Then I got my diagnosis of ulcerative colitis and the perimeter of the puzzle started to take shape. I kind of had a rough framework for what was happening to my body, but it still wasn’t really working. We tried different prescriptions, added on complimentary diagnoses that weren’t really definitive and tried to cram more pieces together unsuccessfully. You could even say that we stuck some pieces in the wrong spots, causing more confusion down the line, but regardless, the perimeter was solid. Then I found the paleo diet and began to understand the connection between what I was eating and the inflammation in my body and some more pieces fell into place. You could even start to make out the picture through the holes.

Then I hit a road block.

I got sick again and it just seemed like the puzzle was doomed. In fact, I had to start taking pieces out in order to find where I had gone wrong. Some of my complimentary diagnoses were misguided and some of my medications were making things much worse than they needed to be. I was about to give up and walk away when I found the autoimmune protocol. All of the sudden a cascade of pieces fell into place. Everything started to take shape. I was addressing the lingering sensitivities in my diet, then I started to address some of the environmental toxins that were possible triggers and I even started to work on managing my stress and my emotions in a healthier way I thought I had this puzzle thing in the bag, until I realized I was still missing the last few pieces.

I couldn’t seem to shake these lingering symptoms.

Why am I Still Not Feeling Better? Troubleshooting on AIPI had a small flare, the result of the stress surrounding a major life change, and after that it seemed that things were still just slightly out of whack. I wasn’t bed ridden like I had been in the past, my world wasn’t falling down around me, I wasn’t really in pain or immobile, I was just not 100%. At first I tried to just wait it out, as if staring at the puzzle for a while would make the pieces magically appear… that didn’t work. Then I started searching for pieces in unlikely places. I wandered away from the perimeter of my autoimmune disease and decided maybe my symptoms were just side effects of medications or some minor, unrelated ailment, which was not the case. Finally, I went back to the original drawing board, the puzzle box, the autoimmune protocol and started to troubleshoot. The Paleo Approach book by Dr. Sarah Ballantyne has a comprehensive troubleshooting checklist in it. I sat down with a pencil and began to work my way through it. I was following the elimination diet, avoiding cross contamination, eating fish 3x per week, eating offal, checking my supplement ingredients, sleeping, managing my stress… I went through the checklist and there was really only three things that came up as possible issues. I could stand to eat more offal, I could try digestive enzymes, and I could get tested for and underlying infections, imbalances, or deficiencies. I poured myself an extra cup of bone broth and decided to look into the concept of digestive enzymes, as I really knew almost nothing about them. I read two helpful articles that I will recommend to you here since I am neither a doctor or a scientist the first was from Dr. Mercola and the second was a resource on the Whole 9 Website

Both of these articles seemed to be in favor of trying digestive enzymes if you were experiencing unresolved digestive issues after changing your diet or if you were dealing with issues surrounding leaky gut. They also seemed to take a just try them and see approach. To be fair, I also read a lot of other articles that stated that no conclusive scientific data existed to support the claim that supplementing with digestive enzymes was beneficial unless you suffered from a severe pancreatic abnormality. Finally, I read a review from a woman who said she had tried them for her fibromyalgia at the suggestion of her naturopath and that they had helped. I decided to give it a try and researched effective and credible brands of enzymes and decided to try this broad-spectrum supplement. I started taking them as directed and to my genuine surprise I could see a notable difference in my overall digestive health within about four days. Just like that, one more puzzle piece fell into place.

My troubleshooting journey is still not over.

I have plans to pursue testing in the near future to rule out or address any lingering hormonal imbalances that may be hindering my healing process, but I have found this process to actually be quite rewarding because it has served as a great reminder that healing through the autoimmune protocol is all encompassing. It is not just about any one lifestyle element or any one part of he picture, it is about putting all of the puzzle pieces back in place. The great news is that most of the time we have all of the information, tools and resources we need right in front of us.

For a full troubleshooting guide I recommend that you purchase either the print or e-book version of The Paleo Approach by Dr. Sarah Ballantyne, but here are a few tips to get you started:

• Are you following all of the recommendations outlined in The Paleo Apprach in regards to diet?

• Are you successfully avoiding cross contamination and exposure to race amounts of gluten and grains?

• Have you double checked your supplements for non AIP ingredients? • Are you eating offal 2-5 times per week?

• Are you eating a variety of foods?

• Are you eating probiotic foods or taking a probiotic supplement?

• Do you avoid eating under duress?

• Are you getting 8-12 hours of quality sleep each night?

• Do you participate in mild to moderate physical activity each day?

• Are you working to decrease stress in your life?

• Have your cortisol levels and thyroid function been tested?


Jesse St. Jean

Jesse St. Jean

I am many things: a wife, a daughter, a sister, a nutritional therapist, a dog-mom… and I’m an autoimmune warrior.


  • You’ve convinced me to do a better job of taking my digestive enzymes. I also need to try offal. Thanks so much for all this information.

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Nutritional therapist Jesse

Hi, I'm Jesse

I empower women autoimmune warriors to reclaim their health by teaching each woman how to make the right food choices to heal her body while confidently owning her journey so she can live a vibrant life with chronic illness.


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