What Is the Best Diet to Reduce Inflammation?

Apr 14, 2024

My Story of Recovery from Inflammation Using Diet

When I tell my story of recovery, naturally, people want to know what I did to feel so much better. For me, diet is key, and I learned this through careful self-observation over several years. I started the Autoimmune Protocol (AIP) about a year before my significant recovery. After that year, I started feeling better, but the progress was slow, and it was very unclear to me at the time whether the diet was contributing to my improvement or was an innocent bystander.

In the years since, I have experimented numerous times with eating foods that are not part of the AIP. In every case, within days to weeks, I begin feeling worse. The most consistent symptoms when I am off the diet are extreme fatigue, pain all over, inflammation (swelling) and an itchy hive like rash.

I’m always amazed at how easy it is to forget what self-management strategies contribute to better health. Each time I start feeling unwell, it takes me some time to remember that it might be due to the diet. Then I start back on the diet strictly again, and it takes a few weeks for the symptoms to decrease and for me to feel better again.


In this blog, you’ll learn:

  • who the Autoimmune Protocol is most helpful for;
  • what the rationale for the AIP is (why it is needed for some people); and
  • what to eat and what to avoid on the AIP.


Who Is the Autoimmune Protocol (AIP) for?

The AIP eating plan is primarily recommended for people who have autoimmune diagnoses such as lupus, multiple sclerosis, and ulcerative colitis. Autoimmune (AI) diseases have many causes. Some of those factors are things such as our genetic sex—things we can’t change. See the blog … for more on this. And some causes like what we eat, we can change.

The Wahls’ diet, recommended by neurologist Dr. Terry Wahls, is one version of the AIP and is showing promise for people with multiple sclerosis (MS). MS is a devastating AI disease in which the brain attacks the myelin sheath of the neurons and makes them ineffective at transmitting nerve signals from the brain to the body.

So, is there anything we can do to decrease risk of autoimmunity or even to improve our health if we already have an AI condition?

The answer is YES. Our diet and gut health are central to autoimmunity, and we have significant influence over our gut health through diet. What we eat impacts the health of our intestines, our bodies, and our microbiome (the bacteria which live in our bowels).


 What Is the Autoimmune Protocol Diet?


The premise of the Autoimmune Protocol is to:

  • Eat a diverse, nutrient-dense
  • Avoid foods that are highly immunogenic (they unduly activate the immune system).
  • Note that people who are vulnerable to autoimmune disease may react to smaller amounts of molecules than people without this vulnerability.
  • Avoid foods which damage the gut.


This is a huge topic area, so, in this blog, I’m going to highlight a few of the strategies to improve gut health, decrease inflammation, and calm autoimmune disease. As of today, there have been no large-scale studies of the Autoimmune Protocol, only small studies with hopeful outcomes.


How Does Nutrition Affect Autoimmune Diseases?

 Many studies show a connection between poor nutrition and autoimmunity however, it is unclear whether:

  • poor nutrition increases the risk of developing an autoimmune disease,
  • people with autoimmune diseases have fewer resources and energy to eat well, or
  • the correlation is caused by some other factor entirely.

The VITAL study published in 2022 found that supplementing with low doses of Vitamin D (2000 IU daily) and omega-3 fatty acids (1000 mg/day) decreased the risk of developing autoimmune disease in older adults. 25,700 older adults were randomized to take the supplements or not, and the incidence of new cases of autoimmune diagnosis was measured for 5 years. Taking Vitamin D decreased the risk by 22% and taking omega-3 fish oil decreased risk by 15%.

 A recent update to this study 2 years after the trial finished showed that 1000 mg/day of omega-3s was still working even if people had stopped taking the supplements.


What Is the Relationship Between Microbiome and Autoimmune Disease?

In my March 2024 blog post, How Can You Improve Your Microbiome, I described the many ways in which the microbiome is essential to health. I explained that a healthy, diverse microbiome is needed to teach our immune system what is safe and what is dangerous. If our microbiome doesn’t get a good start in life as occurs when we are:

  • born by cesarian section
  • bottle fed with formula or
  • require antibiotics for repeated infection,

we are at higher risk of developing an autoimmune disease later in life.

As adults, a healthy microbiome continues to assist with decreasing inflammation. To keep the microbiome healthy, we need to eat a diet rich in diverse, colorful, and fibrous plant-based foods. These foods contain molecules we cannot digest, and the bacteria in our bowel eat these leftovers.

The bacteria use these non-absorbed food particles to produce short chain fatty acids that keep our bowel lining healthy. This decreases inflammation by preventing toxins and pathogens from leaking from the bowel into our body. Note: Our bowel is actually outside our body. If you swallow a marble, it will eventually come out the other end and not interact with your body in any way unless you have a hole in your bowel.


Leaky Gut Is a Trigger of Autoimmunity – What Are the Causes of Leaky Gut?

A leaky gut is thought to be necessary for autoimmunity to develop. The human gut has a surface area about the size of a badminton court, and the integrity of this huge area is critical. If the tight junctions between the intestinal cells become damaged, molecules leak from the inside of the gut lumen, or channel, into the body. When that happens, the immune cells lining the gut view these molecules as invaders and mount an inflammatory response.

There is growing evidence that certain foods and food additives are especially hard on the gut lining and cause leaky gut and inflammation. Some examples include:

  • Lectins found in grain and legumes are difficult to digest. They cause inflammation of the gut lining and the release of a molecule called zonulin and the tight junctions between cells become leaky. Of course, these effects are subtle, otherwise our agricultural civilization never would have thrived. People with autoimmune diseases seem to be more sensitive to lectins than others.
  • High gluten grains. The hybridization of grains such as wheat to increase gluten content may be increasing the problem for sensitive individuals. People with celiac disease are the most sensitive to gluten. Research shows that even on a strict gluten-free diet it can take longer than 5 years for the gut lining to fully heal. This means that, if you try the Autoimmune Protocol diet, even occasional cheating will set you back and you may not see the benefits you are hoping for.
  • Wheat germ agglutinin is part of wheat’s natural defense mechanism against insects. We have difficulty digesting it, so wheat germ agglutinin travels through the entire length of the small intestine wreaking havoc (i.e., causing leaky gut). It activates the immune system directly causing inflammation and oxidative damage.
  • Legumes such as kidney beans also contain high amounts of agglutinins. In people who are sensitive, as few as five kidney beans can cause gastrointestinal distress. Soaking legumes overnight and cooking them slowly over low temperature reduces but does not eliminate the risk of triggering inflammation.
  • Seeds contain molecules called digestive enzyme inhibitors that protect the seeds from being digested in the intestines of animals who eat them. If seeds were digested and broken down, they wouldn’t be able to germinate and perpetuate their species. Digestive enzyme inhibitors are not decreased by cooking. They are also considered to be anti-nutrients as they decrease the absorption of other nutrients. Note that the seeds in fruit and vegetables normally eaten raw don’t contain high levels of lectins and are generally safe even for vulnerable individuals.
  • Nightshades are a family of over 2000 plants that contain molecules called saponins. Saponins have a damaging effect on the intestine and can cause leaky gut. The most common nightshades are tomatoes, eggplant, peppers, and potatoes.
  • Eggs are one of the most common allergenic foods. This is because eggs contain a molecule called lysozyme that is absorbed into the blood and carries with it other proteins that activate the immune system. It is the egg whites that are the most allergenic. Having said this, most people tolerate eggs well. They are a food that can sometimes be reintroduced once an autoimmune disease is in remission.
  • Cow’s milk is one of the most common allergens, especially amongst children. For those who are sensitive, even trace amounts of cheese and ghee can increase inflammation. Most people with milk allergies are aware of it because they experience nasal congestion after consuming milk products.
  • Emulsifiers are a big problem because they directly damage the intestinal lining. I describe this in more detail in my blog on the microbiome. Emulsifiers are added to almost every processed food. Read labels carefully for things such as carrageenan, guar gum, xanthan gum, and others.
  • Diets high in carbohydrates directly cause inflammation. When our cells create energy by burning glucose and oxygen we also create reactive oxygen species which damage molecules and cells. In good health and with a nutrient dense diet, we have the capacity to lessen this oxidative stress, but overeating disrupts the balance and leads to inflammation.


 What is the Autoimmune Protocol Diet?


My daily diet consists of:

  • all vegetables
  • all forms of animal meat protein such as red meat, organ meats, poultry, fish and shellfish
  • all fruits
  • oils from whole foods (e.g., olive, avocado, and coconut)

 I avoid:

  • all grains including gluten-free grains
  • all pseudo-grains for example amaranth, quinoa, Chia, etc.
  • all legumes
  • dairy
  • eggs
  • seeds and seed oils
  • nuts and nut butters
  • spices
  • processed foods
  • sweeteners (nutritive, such as maple syrup or sugar, and non-nutritive, such as Stevia and aspartame)


Cheating and Hacking Don’t Pay Off

Most people who consider a restricted eating plan immediately try to find ways to hack the system. They try to find ways to eat foods they are used to and enjoy but which aren’t on the plan. Over the past 7 years, I’ve learned that doesn’t work for me. I buy, prepare, and cook fresh food every single day. This has required a change of mindset that I need certain foods such as breakfast cereals, desserts, spices, and sauces. Before the modern industrial era, there was no such thing as breakfast cereal, and people were healthy.

Keep in mind that everybody is a bit different. Some people tolerate caffeine. I seem to be fine with nightshades but am very sensitive to spices, which are ground up seeds. When I’m travelling and have limited food choices, I rely on eggs, bacon, and fruit for breakfast. When available, I prioritize high quality food such as organic grass-fed meat and wild caught fish.

Which brings up the issue of cost. The Autoimmune Protocol diet is a bit more expensive than eating processed food, especially if you choose to eat organic. I’m hoping that what I spend on food, I will save on health-related expenses that would accrue if I was in a state of fatigue, constant pain, and inflammation.


Autoimmune Protocol Diet: A Beginner’s Guide

Can You Drink Alcohol on the AIP diet?

Alcohol is not recommended on the AIP diet for a few reasons. First, alcohol is a toxin to the liver and the brain, both organs we need functioning optimally. Second, many healthy eating plans make the recommendation to not drink calories, even healthy calories like fresh squeezed juices increase intestinal permeability and causes leaky gut.

What Sweeteners Can You Have on the AIP diet?

Non-nutritive sweeteners are substances that taste sweet but don’t contain calories. They include things like aspartame and sucralose. Research suggests that because they are sweet, even sweeteners with no calories because the same hormonal and brain responses as sugar. This can result in high insulin levels in the absence of high blood sugar.

Can I Drink Coffee on the AIP diet?

Taken in moderation i.e. one or 2 cups of coffee in the early part of the day, coffee probably isn’t detrimental unless it causes you symptoms. However, the caffeine in coffee can give an artificial sense of energy which can make pacing more difficult. I would recommend avoiding coffee at first and then adding it back while carefully observing for any adverse effects.

What the Heck Can I Eat?

Most people eat a small number of the same foods every day. So, when they are told to avoid whole categories of food they panic and wonder how they will survive on this small number of foods. But it only takes a quick trip to the Internet typing in things like “lists of vegetables”, “lists of fruits” or “lists of meat and offal” to find pages and pages of options.

What about Non-alcoholic Drinks?

As I already mentioned, for metabolic reasons it is good not to drink too many calories. Drinks recommended in the AIP diet include water, herbal teas, coconut water, Kefir, kombucha and green juices.

If you are considering the autoimmune protocol and would like to learn more, I recommend the Paleomom blog by Dr. Sarah Ballantyne PhD. She herself has recovered from multiple autoimmune diseases using the diet and her website and books are filled with great recipes and tips.



In this blog, I’ve explained what autoimmune diseases are and given the rationale for trying the Autoimmune Protocol if you have one of these diagnoses. Many of us may not even be aware that we have an autoimmune diagnosis. I don’t have any abnormal blood work or formal autoimmune diagnosis. And yet the Autoimmune Protocol has been a game changer for my health since 2017. So, if you’ve tried everything else it may be worth giving the AIP a try.

It is difficult to estimate how long it will take on the AIP diet to see benefits. Some people say a trial of a year is necessary. It took me a year and half before I suddenly started feeling better. So, if you try the diet, don’t give up too quickly.

To learn more, join my live online sessions called Live! with Dr. Stein. Held every two weeks, these sessions provide actionable management strategies for people with chronic complex diseases. You will get science based information and the chance to ask your questions of me and my growing community of life long learners. Subscribers to Live! are granted free access to amazing experts on a wide variety of topics - The Expert Speaker Series is approximately monthly.