Integrative Nutrition Blog

Insights on Autoimmune Health and Inflammatory Conditions

Nutrient Deficiencies & Autoimmune Disease: What They Are and How to Fix Them

Apr 13, 2022 | Healthy Eating, Inflammation & Autoimmune Disease

Guest author: Jillian Chacon, graduate student at San José State University

More than 24 million Americans live with autoimmune disease, yet people are struggling with autoimmune symptoms now more than ever (1). When it comes to improving your symptoms, restoring your immune system, and reducing inflammation, your diet is key. However, nutrient deficiencies tend to be more common in those with autoimmune diseases, but why is this? We know that inflammation plays a large role in the immune response to protect against invaders. In the short term, this is helpful, but with autoimmunity, your body becomes chronically inflamed. Surprisingly, 70% of our immune system is in our gut which also happens to be the site of nutrient digestion, absorption, and transport. 

There are many ways nutrient deficiencies are common among autoimmune diseases. Since the majority of our immune system is in our gut, autoimmunity limits the ability for proper digestion, absorption, and transport of nutrients. Not to mention, the constant usage of these nutrients in immune function, metabolism, and more can cause further depletion. 

How do you fix them?

Addressing nutrient deficiencies is critical in improving autoimmune symptoms. By restoring your nutrient status, your body will have the building blocks to strengthen your immune system, repair damaged tissue (like the gut lining), and support your metabolism. Although it’s possible to have any nutrient deficiency, the most common nutrient deficiencies linked to autoimmunity include vitamin D, vitamin A, omega 3 fatty acids, B vitamins, zinc, and magnesium. 

Increasing these nutrients through whole foods is the best way to consistently build long-term nourishment. While supplements may help in the interim, we want to find a way to incorporate these nutrients daily from real foods. The standard American diet is typically devoid of these nutrients that are essential in tackling autoimmune disease. The good news is that there are many ways to take action for your health and include whole foods in a way that is enjoyable and sustainable for you.  

Vitamin D

Vitamin D is commonly thought to play a role in bone health with calcium, but its importance goes far beyond bones. When it comes to autoimmunity, vitamin D functions in anti-inflammatory, antioxidant, and immune system-enhancing ways. More than 42% of Americans are deficient in vitamin D. With more and more Americans working in-door jobs, it can become difficult to obtain adequate vitamin D from the sun. The best sources of real-food vitamin D are:

  • Egg yolks
  • Salmon
  • Sardines
  • Fortified milk
  • Fortified yogurt

Vitamin A

Like vitamin D, vitamin A is a fat-soluble vitamin that has been linked to autoimmunity. It has been linked to rheumatoid arthritis, lupus, and type I diabetes (2). Why is this? Vitamin A enhances immune cell production and is involved in immune cell signaling. Vitamin A deficiency is common with autoimmunity because of the chronic immune response that occurs throughout the body. 

When it comes to vitamin A in the diet there are two forms. Pre-formed vitamin A, like vitamin D, is found in animal foods. Provitamin A is found in fruits and vegetables. Food’s high in vitamin A include:

  • Beef liver
  • Salmon
  • Dairy products
  • Green leafy vegetables
  • Papaya
  • Squash
  • Broccoli
  • Carrots

Omega 3 fatty acids

Omega-3 polyunsaturated fatty acids have been well studied in clinical trials in improving outcomes of autoimmune disease in humans. Some studies even found decrease disease activity and lowered use of anti-inflammatory drugs in people with autoimmune disease (3). Since omega-3’s are important in reducing inflammation, it’s important to consume enough in the diet. Unfortunately, the standard American diet is abundant in omega-6 polyunsaturated fatty acids and low in omega-3’s. The best sources of omega 3’s are:

  • Salmon
  • Mackerel
  • Anchovies
  • Sardines
  • Herring
  • Walnuts
  • Chia seeds
  • Flax seeds

Vitamin B6

Vitamin B6 largely impacts our mood, immune system, cognitive function, and cardiovascular health. It turns out that with autoimmunity there is an increased destruction of vitamin B6 since it is involved in the production of proteins involved in the immune system and helps direct the actions of white blood cells. Decreased B6 can lead to a lowered production of antibodies needed to fight infections. Vitamin B6 can be found in both animal and plant foods, however, it is found in higher amounts in lean animal proteins.

  • Tuna
  • Beef
  • Milk
  • Chicken
  • Eggs
  • Carrots
  • Spinach 
  • Sweet potatoes
  • Bananas


Minerals are like spark plugs for our body. Lately, the mineral zinc has earned popularity as an immune-supporting nutrient and rightly so. Zinc is essential for the functioning of every immune cell. It has even been associated with higher risk for autoimmune disease and it makes sense that during a heightened immune response like with autoimmunity, zinc is diminished rather quickly (4). Our body doesn’t store zinc, so getting enough zinc from our diets is crucial. Excellent sources of zinc include:

  • Beef
  • Oysters
  • Chickpeas
  • Hemp seeds
  • Pine nuts


Magnesium is another mineral that has been gaining a lot of traction. The mineral has anti-inflammatory properties and has helped with the treatment of various autoimmune diseases like rheumatoid arthritis and psoriasis. Low magnesium levels have even been seen in lupus, chronic fatigue syndrome, and fibromyalgia. Although many whole foods have magnesium, the majority of Americans are not consuming enough of it (5). Certain plant foods have high amounts of magnesium, which is why consuming a diet rich in various plant foods can likely increase your magnesium levels.

  • Pumpkin seeds
  • Strawberries
  • Spinach
  • Almonds
  • Cashews
  • Peanuts 


All in all, autoimmune disease is taxing on the body’s organs and systems, especially the immune system and the gut. By improving the nutrient status of specific nutrients commonly depleted with autoimmune disease you are giving your body the tools and resources to continue to fight back and heal. Taking small daily steps towards improving your nutrient status is key in feeling better. By including these foods in ways that are enjoyable to you can make it easier to sustain. If you need help managing your autoimmune diseases and reversing those pesky nutrient deficiencies, please book a free call with Annie to learn about her approach.

You can also follow her on Instagram at @the.autoimmune.dietitian or Facebook at @annierubinnutrition or her website.


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