How An Autoimmune-Paleo Nutritionist Eats

Blog, Lifestyle


In the clinic I work at, we recently started to carry Spectracell testing. I was super excited because Spectracell tests MTHFR genes which can inhibit methylation pathways in the liver and wreak havoc on many body systems. I decided since I am a nutritionist and I tell people all day long what to eat and why,  I should get my nutrients tested and put myself under a bit of a microscope. I have to go back and get my MTHFR gene tested, but my results are back for the micronutrient testing. The reason I like this kind of testing is because Spectracell uses lymphocytes to test a 4-6 month window of nutrient status. Instead of a localized snapshot like a normal blood draw, they use a big window to find trends. And find mine they did!

My results are overall great. I scored above average on antioxidant activity and immune activity (all those extra antioxidants I take are paying off!). The lows however where frustrating. I think part are genetic and the other part are due to diet. Here are the nutrients I was low in:

Low: Calcium, Chromium, Zinc and Glucose/Insulin Metabolism

Now on first glance, the glucose/insulin metabolism could be because of the chromium deficiency. I don’t eat processed carbohydrates or white sugar, so overall my glycemic load is low. I do eat raw chocolate with honey or coconut sugar once every other day or so. I also eat coconut ice cream that is sweetened and an assortment of starchy carbohydrates like squashes.

But, calcium and zinc was bothersome for me. I eat a lot of red meat for zinc, but calcium is not in high supply in the AIP diet. Another thing that I need to say clearly as a disclaimer is that low gastric acidity can cause calcium malabsorption. So I thought I will give you all a glimpse into my daily intake of both supplements and nutrients. I take A LOT of B-12 and Vitamin D (remember, I treat myself as having an autoimmune disease due to have an identical twin with it, so I just plan on autoimmunity as some point and if I curb it, then great) and both those levels were in the low-normal category. The more and more I do this lifestyle and diet, and carry clients through it, the more I come to the conclusion that THE AIP DIET IS NOT ENOUGH WHEN YOU HAVE AUTOIMMUNE DISEASE TO PROPERLY SUPPORT THE IMMUNE SYSTEM.

So here is my day:


6 chicken apple breakfast sausages

2 scoops Apex Energetics Clearvite PSF

6,000 mg. cod liver oil with Co-Q-10

8,000-10,000 iu emulsified D3 with co-factors (A, B6, biotin, cal, mag, k2)

300-400 mcg b-12 as methylcobalamin)

Apex Adaptocrine (adrenal support)

Apex Glysen Synergy

Adrenal Tonic (blend of adaptogenic adrenal herbs I make in my office)

Antioxidant (alpha lipoic acid, green tea extract, turmeric)

HCL digestive support

part-time supplements (30% of my month I take the following):

Apex Repairvite

Apex Hepatosynergy

Apex Liposomal Turmeric


piece of fruit


Leftovers like roasted vegetables, sausages, soups

Snack: apple usually


Stew, stir fry, oven roasted vegetables, soup, steak, salad, roasted chicken, roasted squash

Dessert (If I have any)

Piece of raw chocolate or coconut ice cream

Here is what I don’t eat a lot of on AIP: organ meats and bone broth. Could that be the missing micronutrient piece for me? Perhaps! I eat bone broth with soups and dinners when I cook, but I don’t seek it out and drink 1/2 cup a day, (mostly because I don’t have a lot of time to make it!) But, there is no vegetable I don’t eat or that I actively stay away from. I will eat a starchy vegetable like squash or sweet potato a few times a week. Tonight for example, my sister is making us brussel sprouts with bacon and turkey sausage. In addition to what I eat, I would estimate there is 2-3 tablespoons of fat in the form of saturated animal fat, coconut oil or olive oil per day. I drink fermented beverages like kombucha or kefir water a few times a week as well. And that is it folks! So what now? Well, I ordered a calcium supplement and I am increasing my HCL digestive pills to increase the absorption of the calcium.  (I have no ulcer history so I use these). I also ordered Glysen Synergy from Apex for chromium, zinc and blood sugar control. I am rounding out the great diet I am on with extra nutrients. I am paying even closer attention to limiting my starchy carbohydrates and occasional sweets.

Could the AIP cause low zinc or calcium? Perhaps. Could my particular body type not metabolize calcium or zinc and therefore I am not absorbing the calcium I am eating? Yes. Could I be deficient in zinc and calcium because I don’t eat enough? Yep. Could it be a combination of all three of those factors. Yes, and I think that is the theory I am leaning towards. My grandmother had osteoporosis and two hip fractures late in life, so I know I have a predisposition. My sister and I have pieces together that she probably had celiac and a known lactose intolerance. My father most likely has Hashimotos and was probably misdiagnosed with Graves Disease in his 30’s. I take those factors into consideration when I think about my genetic disposition.

So, in summary:

1. The Autoimmune Paleo Diet is not enough by itself to support putting Autoimmune Disease into remission. In almost every case (the blood work I see of dozens of clients each week for example proves this) points to the fact that this diet is not sufficient alone. Supplementation is almost always called for various reasons (anemia, SIBO, hormone imbalances, lack of digestive enzymes or HCL, thyroid support, pituitary support, blood sugar control)

2. The AIP diet (like most restrictive diets) may have some general leanings towards micronutrient deficiencies

3. I need to embrace organ meats and make more time to prepare bone broth for myself

4. Even those with a “perfect” diet can have deficiencies and it is very likely

5. Another reason why most people really need the help of a skilled practitioner who has a broad understanding of micronutrient deficiency states as well as an understanding of how to translate lab work into micro and macronutrient deficiency pictures


  1. Karen Horn

    Great article! Is there someone on the web to find doctors who treat AIP with diet and suppliments? Thanks!

    • Jessica Flanigan

      Karen there is and they have a list. Datis Kharrazian has a list on his website. And, I do too!

  2. Alla Yeliseyeva

    i'd like to argue that AIP is not high in calcium, it's what you make of it. calcium is high in winter greens and sardines – those are the most potent sources, more potent than dairy which I'm assuming you're referring to when saying AIP is not high in calcium. for one to have adequate amounts of calcium absorbed co factors like vit D vit A and vit K should be abundant. Calcium in sardines with bones – 382, in figs – 300, in hard cheese – 331, cooked collards – 220, cooked spinach -240. I hardly think you can blame it on AIP

    • Jessica Flanigan

      Alla, sorry I did not reply sooner; I was not getting comments in my inbox! I totally agree with you. I tend to not eat AIP foods that are high in calcium and it is what you make of it. I think it could have been better phrased to say more along the lines of “be mindful of calcium sources on AIP to be sure you are getting enough”. Jessica

  3. Samantha

    Are you currently taking clients?

    • Jessica

      Hi Samantha! Yes I am. Here is my contact email: send me a note and I will give you the details 🙂 -jessica

  4. lisa hreha

    i was concerned about calcium. I have not done much dairy in a long time and osteporosis runs in my family. I probably didnt spell that right. I was concerned and I wanted to take a supplement but dont know which one. Can you recommend one and something for my adrenal. Unfortunately I cant afford so many like you seem to do ? The thought of organ meat totally grosses me out and I just dont want to mess with bone broth. I probably could make the time but I am trying to just keep it simple. I am 48 and premenopausal plus have had Hashi’s for 25 years but only seem to have issues in the past few years. Its like my symptoms have been dormant or its just an age thing. Not sure really which. Thanks

    • Jessica

      Hi Lisa! Great questions! They would need to be addressed in a more formal matter by me or by your alternative health care practitioner. There are a number of adrenal supplements out there to choose from. If you want to pm me: if you would like to set up an appt! -jessica

  5. Sarah

    Hi, Jessica!

    I’ve been following your blog ever since last year when I first was diagnosed with subacute-CIDP at the age of 25.
    I’ve just recently been diagnosed with having osteoporosis in my hips (no fractures yet), but my calcium levels (blood testing) are OK (despite the fact that I due to my food map-sensitivity+keto-approach to the aip-diet) haven’t been consuming calcium in the way that I ought to). The only paleo nutrionist that I could find in my area (I’m residing in Sweden, Europe) strongly advised me to not take any kind of calcium supplements because they are prone to create “plaque”, and so now I’m scared of supplementing with calcium even though thats what western medicine thinks I should do. I’m already taking Vitamin D, but what about my calcium? What do you think I should do? and also, what is the name of the calcium supplement that you are using?

    I really, really, really would appreciate your input.
    Due to my neurological illness, I’m on intravenous immunoglobulin (IVIG) and so I really can’t risk getting any plaque because then the chances of me actually developing any kind of cloths/thrombosis are pretty significant.

    Kind regards, Sarah

    • Jessica

      Hi Sarah! For legal reasons, I cannot give supplement advice over the internet. I am so sorry! -jessica

  6. Elisabeth

    I follow the AIP diet. I track and macro and micronutrients with Chronometer. The only days I manage to get above 800mg calcium are when I eat canned salmon with bones. But I simply don’t want to eat canned salmon every day. Yes, it’s possible to get enough calcium on the AIP diet, bit I suspect that the majority don’t. I’m considering making my own fortified tigernut milk.

    • Jessica

      Great points. Thank you for sharing!


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