Is the autoimmune paleo (AIP) diet making you feel worse?

Autoimmune paleo diet

feel worse AIP diet copy

Although the autoimmune paleo (AIP) diet is a well known foundation for managing Hashimoto’s hypothyroidism, some people are dismayed to find embarking on it makes them feel worse. What gives? The sudden change in diet can temporarily upset your chemistry and reveal hidden health problems.

If you have been accustomed to eating gluten, dairy, grains, sugars, and processed foods, going cold turkey off those foods is a radical shift. Likewise, adding in lots of vegetables can also shock a digestive system unaccustomed to ample plant fiber.

Most people find the AIP diet significantly improves Hashimoto’s hypothyroidism. If you’re not one of them, however, don’t give up on the diet. Instead, look for the underlying reason why.

Feeling temporarily worse on the AIP diet to manage Hashimoto’s hypothyroidism

Here are some common adverse reactions to the autoimmune paleo diet. Knowing why you react negatively can further help you on your wellness journey.

  • Low blood sugar. Symptoms of low blood sugar and adrenal fatigue can worsen on this diet. This is usually caused by not eating enough or frequently enough. The general recommendation is to eat every two to three hours, however, some people may initially need a bite or two every hour until blood sugar stabilizes and they can go longer without eating. Avoid sugary fruits and investigate what else may be taxing your adrenal function, such as brain-based issues, autoimmunity, or chronic infection.
  • New food sensitivities. When gut damage is bad and inflammation high, it’s possible to develop food sensitivities to new foods on the autoimmune diet. This is very frustrating for people as the diet is already so limited. This can be a complex situation that requires concerted effort to tame inflammation and repair the gut.
  • Opioid withdrawal reactions. Opioids are morphine-like chemicals made by the body that reduce pain and create a feeling of euphoria and well-being. Some people become dependent on foods that release opioids in the brain, namely gluten and dairy. They can initially experience depression, anger, lethargy, and agitation on the autoimmune diet. For those with serious opioid addictions to gluten and dairy, withdrawal can be intense.
  • Brain chemical imbalance. A diet high in processed carbohydrates affects brain chemicals that influence our mood, particularly serotonin and dopamine. Suddenly switching to a lower carbohydrate diet can disrupt the balance of brain chemicals and cause temporary changes in mood, behavior, and personality. You may need to gradually lower carbohydrate consumption if so.
  • Insomnia and anxiety. Some people report irresolvable insomnia and anxiety if carbohydrate consumption is too low. If these symptoms persist long after an adjustment period, you may simply need to use trial and error to find the carbohydrate “sweet spot” that lets you sleep but also keeps blood sugar in check.
  • Difficulty digesting fiber. The AIP diet is heavy on vegetables. For those with compromised digestive function, this can overwhelm the gut. Concerted gut repair nutritional therapy can ease you into a higher fiber diet.
  • Histamine intolerance. This is a reaction to aged or fermented foods that causes myriad symptoms, including rashes, runny nose, or headaches. Avoiding these foods for a while can help the gut heal so you can eat them later.
  • Yeast and bacteria die-off reactions. Going cold turkey off processed carbs, gluten, and dairy can cause a sudden and uncomfortable die off of harmful yeast and bacteria in your gut. This is especially true in the case of poor liver detoxification and constipation. Supporting the body’s pathways of elimination can help. Hashimoto’s hypothyroidism is known to compromise detoxification capacity so supporting that can be very helpful.

These are a few of the issues that can arise when you switch to the autoimmune paleo diet to manage your Hashimoto’s hypothyroidism. (Don’t forget to consider the grief and anger you may feel about missing your favorite foods.) However, if you weather the transition and ferret out sources of discomfort, your improved thyroid health will more than make up for the rough legs of the journey.

Contact our team to learn more about diets and supplements that are tailored to your condition!

Joni Labbe

About Joni Labbe

Dr. Joni Labbe is a board-certified clinical nutritionist specializing in science-based nutrition with a focus on women's health issues. She has successfully helped pre-menopausal and menopausal women regain and maintain their health since 1995. Dr. Labbe is the author of the Amazon #1 Best Selling book Thyroid & Menopause Madness and It’s Not Just Menopause: It’s Your Thyroid. She is also a professional speaker, radio personality, fitness expert, and former host of “Healthier Way With Dr. Labbe.” Dr. Labbe is one of the country’s leading authorities on thyroid disorders, including Hashimoto’s disease. Dr. Labbe has also authored numerous articles and blogs on health, nutrition, and thyroid health, as seen in Naturally Savvy, Thyroid Nation, and Fox News. She is a Board Certified Clinical Nutritionist, Doctor of Chiropractic, and has post graduate training in Functional Neurology, Functional Endocrinology, Functional Blood Chemistry Analysis, and earned a Diplomate and Fellow in Nutrition from the American Association of Integrative Medicine.


  • Andrea says:

    Good day from the UK!

    I am on a lchf diet to reduce/reverse insulin resistance after continually gaining wait over the last 5 years. As good nutrition is quite new to me, (apparently I have been eating wrong my whole life) I am researching day after day to understand why my liver, pancreas, gallbladder etc are failing me. Then I came across the AIP diet which is completely different to the keto type lifestyle but supports Hashimotos which is suspected of being undiagnosed for 40 years. Also I’m in the initial stages of menopause (I think) and just don’t know where to go from here.

    • Dr. Joni Labbe says:

      I believe the best place to start is to find a Functional Health Care Practitioner in your area that would run extensive blood work, such as a CBC with Differenitals, A full metabolic panel, a full thyroid panel (that includes the TPO and TGB antibodies) to determine what the root causes of why you are having liver, pancreas, gallbladder issues. From there, the functional health practitioner can determine what further tests you might need, what supplements would be best, and what the most advantageous diet would be for your particular needs. The AIP diet and the keto type diets are both good depending on what your particular lab work says about you. You don’t want to waste time and resources on one diet if you need another. The diet comes second to the lab work so that the proper diet can be recommended. Examples of other diets include: anti-inflammatory (if we see inflammation markers), a diet for anemia, a diet if we see a history of seizures, and so many more options.

      Another thing to consider is that your health issues may not be related to diet, but to imbalanced hormones, gut issues, auto immune problems, or adrenal fatigue. Unfortunately, I don’t have a referral for anyone in England. We normally could do remote consultations with you and provide you with the above, if you were located in the US. Please reach out if you find yourself anywhere in the US, as we would be glad to help you find the science-based answers to your issues.

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