paleo diet | Integrative functional medicine blog

When would an Autoimmune Paleo diet make you feel worse?



paleo diet

There are many diets available for lots of different conditions, people, and goals. One of those diets is called the autoimmune paleo diet, or more commonly known as the A.I.P. diet.

Although the autoimmune diet is a well known foundation for managing chronic health issues, 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 and sometimes the body doesn’t like those changes even when they are good for you. Think of an addict going off of whatever their vise is.

Likewise, adding in lots of vegetables can also shock a digestive system unaccustomed to ample plant fiber. Your body can go through withdrawals and sometimes experience what is known as a herxheimer reaction. Not very pleasant but usually fairly short lived. More on this below.

Most people feel significantly better on the autoimmune diet. If you’re not one of them, however, don’t give up on the diet. Instead, look for the underlying reason why. Here are some common reasons you should be looking at:

#1 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. Adrenal function is a huge factor in how our hormones are functioning so be careful.

#2 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 many times due to what many people know as leaky gut. 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. In this situation I really recommend getting tested to see what your sensitivities are and come up with a food rotation diet in order to reduce the amount of food sensitivities you may get.

#3 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. This is fun for neither the “addict” or the family and friends in the near vicinity.

#4 Brain chemical imbalance.


A diet high in processed carbohydrates affects brain chemicals that influence our mood, particularly serotonin and dopamine. Depending on which neurotransmitter we are talking about 60-90% of neurotransmitters are produced in the gut. 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. I always have patients go low and go slow. Better safe than sorry.

#5 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. The body, or more importantly the brain does need some carbohydrates to function. If your system is not quite balanced you may need to keep some carbs in the diet for a little while longer. But only a little.

#6 Difficulty digesting fiber.

The autoimmune 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. This is often linked to the health of your gut.
Click here for more info on gut health.

#7 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. There are certain foods that tend to be higher in natural histamine levels. If you have allergies it might be a good idea to look these up and test the waters with these particular foods just to make sure they don’t make things worse.

#8 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.
Remember the herxheimer reaction? This is especially true in the case of poor liver detoxification and constipation. Supporting the body’s pathways of elimination can help. Check out my page on detoxification. Also, I would like to point out that the last step of detoxification is elimination (pooping). If your digestion isn’t functioning properly then you cannot detoxify properly.

These are a few of the issues that can arise when you switch to the autoimmune diet. 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 newfound health will more than make up for the rough legs of the journey.

Be healthy, be happy,
Dr. Craig Mortensen


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