The Best Diet for Autoimmune Disease

Published on: 01/26/2021

What is the best diet for someone living with autoimmune disease??

I see this question ALL THE TIME! The truth is, there is not one diet that works best for everyone living with autoimmunity because every one of us is unique.

The “best” diet needs to be personalized just for you because:

  • Your genetics influence how your body processes and absorbs nutrients from food
  • You have your own personal likes and dislikes when it comes to what you eat (and probably some really strong opinions about these!)
  • What you can buy from the market is different depending on where you live and what season it is
  • You can have other health conditions or sensitivities that impacts how you tolerate foods

The list of what makes you unique can go on and on.

So, while going vegan might help one person, it may cause nutrient deficiencies in another. Someone might say “Keto is the bomb!”, but another might say “Keto makes me feel worse!”. The Paleo enthusiast might say “I feel so much better eating like our ancestors!”, while the Paleo detractor would say “Red meat makes my joints hurt!”.

There are so many ideas and opinions around the best diet for autoimmune diseases, or any chronic disease for that matter, that it makes my already foggy brain feel even foggier!

That being said, I do believe that there are a few key dietary principles that contribute to healthier living. These principles apply across every type of diet and every type of autoimmune disease. (Ok well, maybe not the Carnivore diet)


By following these guidelines for eating, you can greatly reduce inflammation, which is important for reducing autoimmune symptoms and flares.

Let’s break down these principles…


What this means is to choose unprocessed foods more often. Things like fresh or frozen fruits, vegetables, meat, eggs, nuts, grains and other foods that don’t come in a box, or are combined with a long list of questionable ingredients.

I love the book “Food Rules”, by Michael Pollan.(1) Some of the rules he writes in his book perfectly outline how to choose real foods:

  • Avoid food products that contain more than five ingredients
  • Avoid food products containing ingredients that a third-grader couldn’t pronounce
  • Avoid foods you see advertised on TV
  • Eat only foods that eventually will rot
  • Eat only foods that have been cooked by a human

The reason that plants come in so many different colors is that they contain compounds that they use to protect themselves from dangers such as animals, bugs, germs and even too much sunlight. When we eat plant-based foods, those same compounds, called phytonutrients, will similarly protect us from danger. For example, phytonutrients can fight harmful toxins, microbes, damaging free radicals and thereby reduce inflammation.

Consuming phytonutrients can lead to decreased incidence of cancers and many chronic diseases like heart disease, autoimmunity, diabetes, and more. What’s more, each color represents different phytonutrients with different actions. So when we eat a rainbow of different colored plants, we get a broad range of protection against a variety of dangers to our health. Eating more fruits and vegetables has even been shown to improve feelings of happiness and well-being! (2)

Tips for Getting More Colors
  • Aim for at least 3 colors of plant foods with each meal
  • Vary your choices so that you’re not eating the same foods over and over again – try a new vegetable and a new fruit every week!
  • Substitute your usual neutral colored foods with some color. For example, substitute a vibrant orange sweet potato or purple yam for your boring white baked potato.
  • Mix multiple different fruits and vegetables into a delicious smoothie

Carbohydrates are organic compounds containing carbon, oxygen and hydrogen molecules (thus the name, carb-O-hydrate). They are an important source of energy for our bodies and come in many different sizes. Most carbohydrates (aka “carbs”) need to be broken down by our bodies into small molecules called glucose in order to be used as energy. Larger carb molecules are called complex carbs and smaller molecules are called simple carbs. Complex carbs take longer to be broken down by our bodies and utilized for energy. These are usually found in fruits, vegetables, legumes, nuts, seeds, and whole grains. Sugar usually refers to types of simple carbs and includes ingredients like glucose, fructose, white sugar, brown sugar, coconut sugar, corn syrup and others. Many of these simple carbs are mechanically refined or processed.

The problem is, when we consume more carbohydrates than our body actually needs, our body efficiently stores that extra sugar away to be used later. This is a throw-back to our cavemen ancestry, when food was less abundant, and it could be days or weeks before the next successful hunt. Unfortunately, that excess sugar becomes converted to and stored as fat, causing many people to become overweight or obese. Furthermore, too much carb intake can trigger inflammatory processes in the body. This is particularly the case with the consumption of simple sugars. Inflammation can cause a plethora of undesirable symptoms and contribute to the development of many diseases.

Tips for Reducing Excess Sugar and Refined Carbohydrates
  • Reduce the amount of soda, juice and sweetened beverages that you drink; choose plain water or unsweetened sparkling water, instead
  • When choosing foods containing grains, opt for items containing whole grains (including the bran)
  • Use fruit to sweeten foods instead of sugar or syrup. For example, cut up berries and add to plain oatmeal, yogurt or whole grain pancakes.
  • Choose fruit more often when you’re craving something sweet
  • Choose dark chocolate instead of milk or white chocolate
  • When making recipes for cakes or muffins, cut the amount of sugar or sweetener, or substitute with applesauce or bananas. Substitute whole grain flour for some of the white flour.
  • Be mindful with how much ketchup, barbecue sauce or other condiments that you add to food, as many of these are high in sugar
  • Always read food labels and avoid products with any form of sugar as one of the first three ingredients

Follow these 3 Eating Principles and you will be well on your way to improving your health!


1. Pollan, M. Food Rules. New York, NY: Penguin Books; 2009.

2. Minich DM. A review of the science of colorful, plant-based food and practical strategies for “Eating the Rainbow”. Journal of Nutrition and Metabolism, 2019; Article ID 2125070.


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Hi! I’m Dora – an unconventional pharmacist turned functional medicine nutritionist. I’m also a mom of twins and an autoimmune warrior.

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