When You Don’t Get Better On The AIP Diet

Blog, feature, Lifestyle


I hear this quite a bit on Autoimmune Paleo social media: “I am not feeling as good as I want on the AIP diet”. Maybe you feel marginally better? Or maybe you feel quite a bit better but not as good as you want? There can be a number of reasons for this. Using an experienced practitioner is key when this situation arises.

I complied a list of what may be happening when folks go on AIP and don’t feel as good as they should:

1. There is a food in the AIP diet they are sensitive to

2. Their liver detoxification pathways are not robust enough

3. Digestive function has not been restored

4. Inflammation has not been properly addressed

5. An infection that has not been diagnosed (like SIBO, virus or dental infection)

6. The Brain-Gut axis is impaired and has not been repaired

7. The Hypothalums-Pituitary axis is impaired and has not been repaired

8. Endocrine disruption in form of hormone imbalance or adrenal dysfuntion

9. Emotional/Heart component of the Autoimmunity has not been examined

10. Micro or Macro Nutrient deficiencies

11. Blood Sugar Issues are present and are related to entire endocrine system and brain function (even while Paleo!)

12. You have an undiagnosed anemia

So which way to go? Well, if someone is not or does not know how to look at lab work, and food is the only piece being examined, it is only including part of the picture. If for example you see a moderately elevated MCV (mean corpuscular volume) on lab work, how would your practitioner proceed? When might they consider sending you to a doctor to rule out pernicious anemia? What if you have undiagnosed hemachromatosis and a well meaning health coach strongly suggests adding organ meat to your diet. Would that be contraindicated? How would they tell the difference between moderate and mildly elevated liver enzyme markers? How do the role of bio-identical hormones play a negative role in autoimmune disease? Are probiotics improving function or hindering it? How long should you be on digestive support? Why look at sodium markers on routine lab work? How can memory impairment be related to Autoimmune Disease and how can it be supported? What if you go on the AIP diet (like I did for a year) and you still have Insulin Resistant Hypoglycemia? Then what?

You can eat as much liver pate and bone broth as you want but if you are not improving function or absorption, then is it useful? Liver pate may very well eliminate micronutrient lows, but does it matter if one is not addressing the impaired integrity of the intestinal mucosa? Does a low inflammatory diet alone heal the intestinal mucosa? Does bone broth with natural levels of l-glutamine repair the intestinal mucosa? What is the role of adrenal glandulars and adrenal adaptogens? Do they go together? Should they be taken apart? What about the cytokine pathways? Are they relevant? What about the role of Nitric Oxide in your autoimmune disease. Should that be addressed? If you have a high homocysteine level, should you test for the MTHFR gene? Or just take methylated folate and B-12? What if you have an autoimmune disease AND an active viral infection. What do you do then?

Above is just a sliver of the normal everyday issues I observe clinically with AIP clients. These are the extremely relevant issues that can go along with the Heart-Mind-Body issues that can be at the very root of Autoimmune Disease. These are critical questions to ask and critical questions that need to be addressed in my opinion. You can’t heal the thyroid without looking at the brain. You can’t heal the brain without looking at inflammation. Autoimmunity is a truly multidisciplinary approach.

There are a multitude of factors that go along with health, healing and the Autoimmune Paleo diet. Having a visionary approach not only helps you sort through the complexities of what you are facing, but helps to streamline the path to healing. Who is your team? What is their approach? How far are they willing to go to get you to where you need to go? There is a great divide in the healing world around autoimmunity. A number of practitioners are emerging that know about the Autoimmune Paleo diet and how to support your efforts and physiology while on it. But how comprehensive is their approach? I am lucky that I have had amazing training and count myself in this group of knowledgeable contributors. If you have been doing the AIP diet and you are not feeling better, or as good as you hoped, there are still stones unturned. And if diet is the only component you are exploring, perhaps there is more that could be thoughtfully examined. There are still many, many options out there for you. Don’t give up. The answers are still waiting to be discovered!





  1. Connie

    I’ve been ill most my 60 years. In 1990 diagnosed with Giardia (treated with antibiotics) and celiac disease(terrible diarrhea) and with no Improvement with diet and drugs, diagnosed with IBS. All colonoscopies and endo were clear, had many of these over years. Other tests also neg. from last work up 10 years ago, only suggesting antidepressants. I stopped seeing gastro’s and on my own took an Alcat test for food intolerances and CEDSA test(showing parasites, kidney, gallbladder and adrenals needing support). Did two treatments using some supplements and tinctures(grain based and pill form) but grain based tinctures caused more diarrhea. Parasites still positive on second test. Tried a couple parasite products. I only eat grass fed bison, wild caught fish, some veggies and fruits, bone broth, homemade kombucha, reverse osmosis water, coconut water and coc. and olive oil. I stopped the city fluoride/ chlorine water last June with some diarrhea and leakage stopping. I don’t tolerate vitamins well,especially if derived from grains,soy,rice, pork or beef. I’ve tried gaps stage one for a month, but still have watery, lardy stools. I’m worried I may still have parasites. What do you suggest for treatment, as there are so many products available and different theories on length of treatment and working with full moon. And then there’s the cleanses. I don’t have the insurance I had earlier that covered colonoscopies,endoscopies and other tests(still don’t cover naturopathic doctors) and don’t know where to find an alternative doctor or afford one in my area. They don’t understand leaky gut, food intolerances. I read recovery stories that the people had many tests and seeing several special healers or alternative doctors and wonder how did they afford this. I had to retire last Jan. as time needed to make all my food, my long work hours and too many embarrassing accidents with diarrhea. I avoid traveling as food is impossible and is exhausting(tried last summer and ended up very sick after). It’s also hard to cook regular foods for family and not get to eat it, or have to test taste for seasoning, etc. and get sick. I detest holidays. I keep having more food intolerances that soon I won’t be able to eat anything, which makes me wonder if I still have parasites. Some say it can take a year to heal. I can’t do that stage 1 gaps diet much more. Thank you.

    • Jessica

      Hi Connie! I am not allowed to tell you what treatment may be best, but perhaps finding a ND or functional medical doctor that can do a different stool test on your than the standard ones doctors perform may be helpful? I like Genova GI 2200 Effects 3 days stool test. I find that doing strict diets like GAPS and AIP don’t work with active parasites. And that those diets often won’t get rid of the parasites either. I know there is a cost involved, but it sounds like no one has gotten down to the bottom of this. In CA if the stool test is run through a chiropractor and you have health insurance (Genova accepts most) then the test is only $125 out of pocket for you. I would keep trying at this..sounds like you are getting closer and closer to getting to the bottom of things! -jessica

    • Carolyn

      Hello Connie. I know this has been a year ago but if your still looking for alternative therapies email me. I might be able to help. Carolynwheeler2@gmail.com

  2. Diana

    Hi Jessica,
    What do you mean exactly by inflamation has not been addressed (4)?

    • Jessica

      Hi Diana! Inflammation drivers: AIP-approved foods that you produce antibodies to. Not finding the coinfections: viral, bacterial mostly. Not addressing inflammatory thoughts: “life is against me” or “this disease is more powerful than me” or “I have to fight disease to find healing”.. the gut-brain axis has not been healed so inflammation in brain keeps driving inflammation in gut…just a few that I listed.

      • Katja

        And what can you do to those thoughts? I have a bad inflammatory arthritis in my knees and I’ve been on the AIP diet now for 3 months, they also did food sensitivity test (lots of sensitivities) My knees got a little better but they are still bad, they get swollen one at a time. I also have hashimotos, I’ve has it since I was 6 years old (Im now 24)
        Every time I can feel my knee starting to get swollen I crash emotionally. I just feel hopeless and scared how swollen its going to get again. Its really hard to not think like that when it seems like its not really getting better.
        Im going to test more stuff soon, parasites and hormones and fungus etc. Once I have enough money for it..

  3. Naomi

    Hi Jessica,

    I have terrible problems with inflammation in my knee joints. I also have constant nasal inflammation with no nose breathing at all. I also have hypoglycaemia. I am interested in aip diet, but i am a lifelong vegetarian (no meat or fish) and see I would have to cut out all my sources of protein which are beans, nuts, grains and eggs. Is there any way it can be adapted to vegetarians? I try to control my hypoglycaemia with high protein and zero sugar, but not having a lot of success. Can you help, do you think?

    • Jessica

      HI Naomi! I don’t know a way the diet can be adopted as strict vegetarian. Sorry!

  4. suryabahn singh

    I read your article and its nice.my son have haismotos and we got to 2 years before and his age now 6 & 1/2 and my son also on aip diet since 1 year and since one year we done three bold test and ready for 4 in coming days.

    and while on aip diet my son antitpo reduce from 600 to 150 (but one time he don’t reduce antibody may be there is some supplement he use to take) after taking out that supplement my son antitpo reduce.

    but now again I start noticing some time he ask to eat something after 3 or 2 & 1/2 hours after lunch.
    he have this issue before, but since march he never complains of asking food in between.after luch and in 4 hours we give something to eat.

    and he complains of his shin bone and his arms pain

    I am still looking for this answer .

  5. Amanda Jane

    Hi there,
    I have morphea and recently learned it is an AI. I’ve had it since I was 3 years old…obviously, never diagnosed. I’ve had severe shingles and a terrible time with mercury poisoning a few years ago. I went through IVF treatment in 2013 and then adopted my beautiful daughter at birth and just went through a divorce. Stress and adrenal fatigue has been high for about 10 years. I was also a professional dancer and I have taught pilates and yoga for over 20 years. I am dealing with massive inflammation for my small frame and it feels horrendous! I was following dr axe and his protocol but then added blueberries for the anti inflammatory properties I’ve the summer. I’m wondering if I now cannot tolerate the fructose. My hands and legs tingle and are so tight. I vary weight about 3-5 pounds throughout the day due to the inflammation. It’s tough to teach my clients and be in a fun, enthusiastic mood w them due to this. Ive reached out to dr Ronald Drucker in Florida, as well who had recommended enzymes and flax oil…nothing new. Perhaps I should only consume bone broth and veggies? If it means the inflammation will disappear, ok. I’ve been dairy, refined sugar, grain, caffeine and alcohol free for about five months
    I so appreciate your wisdom and am excited to get your response. Thank you!!

    • Jessica

      HI Amanda! sounds like there is more going on here that has perhaps not been uncovered? My email: info@aiplifestyle.com if you would like info about how we can work together! warmly, jessica

  6. matt

    What about sweet potatoes? I have eliminated every thing on the list but them. I will boil one about small-medium sized to lower the GI.

    I have heard mixed things about them. And of course its very hard for me to go through the day without any type of real carbohydrates

    • Henry

      Why not simply try eliminating them for 30 days and see if that helps?? There are no bad foods other than gluten some even tolerate that in moderation.

      It’s a matter of if it works for you after elminunating it.

  7. Henry

    Hi Jessica,

    It’s intresting you note emotional aspect. It sucks to see that because some of us are worried and just can’t help it because real problems are going and no amount of meditation is going to help it- only relief from the actual problem will because it’s that important.

    I got hit with a series of events with outside family, it was non stop and unavoidable. Shortly afterwards my head felt weird and tense, and have had the worst case of brain fog with a lack of alertness/wakefulness.

    For 8 months I’ve also had lymph nodes swelling but yet my blood work and ct scan show normal other than low/normal B12.

    I can hardly handle any stress either. Since then I can’t handle normal things I’ve eaten like small bits of sugar, fruit, or coffee, or I’ll be almost drunk too. It’s like a switch went off and my body changed.

    I even had to quit work because of this and im not even 40 yet.

    What would you recommend in this situation? Or should I say what could help? Anti -anxiety meds short term?

    I can’t imagine a diet correcting something like this, but I was thinking of trying the Gaps Diet.

    • Helene

      I rly recc’d researching the meds. Theres no shortterm. Benzies, for example, r extremely addictive and h.e.l.l. to get off. Kellybroganmd.com is a good place for other avenues than meds.

  8. Jane

    I am almost to week six of AIP. I have to get blood work done twice a month. Before I started AIP my inflammation levels were looking good. As I’ve continued they have gotten worse and worse, which means the pain has gotten worse. I have chronic disease induced anemia. I also have a serious fungal infection, but those levels have been good for over 6 months now. Really frustrated I wasted 6 weeks eating so restrictive.

  9. Ela

    Dr. Terry Wahl’s book – the Wahls Protocol
    Dr. Gundry’s book – the Plant Paradox
    Both of these MDs have vegetarian and vegan options in their healing protocols and recipes. And both have reversed autoimmune disease. They’re both on all the typical social media options with support groups on Facebook. I had to eventually include bone broth at least to balance my hormones & not die but I completely understand how hard it is to even consider the thought.


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