Integrative Nutrition Blog

Insights on Autoimmune Health and Inflammatory Conditions

Autoimmune Nutrient Deficiencies

Jun 4, 2025 | Inflammation & Autoimmune Disease

One of my biggest concerns when working with autoimmune clients is nutrient deficiencies. Nutrient deficiencies are quite common in my client population. This is because chronic inflammation can more easily deplete vitamin and mineral stores which can ultimately put a strain on the immune system. We are going to discuss this phenomenon, as well as highlight a few key nutrients to be on the lookout for. Plus, learn what you can do to uncover and reverse nutrient deficiencies.

Why do Nutrient Deficiencies Happen with Autoimmune Diseases?

Nutrient deficiencies happen when your body doesn’t have enough of a specific vitamin or mineral to support ongoing needs in the body. In case you weren’t aware, vitamins and minerals are used for energy production, to build and repair tissues and to regulate reactions and processes in the body.

There are a number of reasons why nutrient deficiencies are more common in autoimmune disease. First, inflammation in the digestive tract can impair nutrient absorption. Any gut related autoimmune disease, or anyone with food sensitivities, leaky gut or dysbiosis (which is MOST people) will have inflammation in their gut. Food is how we get most of our nutrients. Therefore, having suboptimal digestion and absorption prevents nutrients from getting into our body to support our body’s stores.

Second, chronic inflammation can affect nutrient absorption. Inflammation can affect how nutrients are transported into cells and make that process less efficient. Inflammation may also contribute to malabsorption issues. Lastly, stress may also lower nutrient absorption. Cortisol, your stress hormone, can slow down digestion and interfere with absorption. Stress also increases your body’s demand for nutrients.

What are Common Nutrient Deficiencies in Autoimmune Diseases?

There are several nutrient deficiencies that are commonly found in people with autoimmune diseases. Here are a few of these and why:

Vitamin D

Vitamin D is the vitamin deficiency I see the most in my client population. This vitamin plays a vital role in immune system regulation and inflammation. In fact, some researchers believe that low vitamin D may be an underlying cause of some autoimmune diseases. And, vitamin D status is indirectly correlated to disease activity. 

Iron

Iron is another common deficiency due to malabsorption and chronic inflammation. This mineral helps red blood cells carry oxygen throughout the body. Iron also supports the immune system and helps with the production of certain hormones. Low iron may cause fatigue, impair endurance and muscle performance, and can increase the risk of infections. 

Vitamin B12

Vitamin B12 is best known for its role in energy metabolism, red blood cell formation, DNA synthesis and nerve function. This vitamin is a common nutrient deficiency because gastrointestinal absorption might be impaired in autoimmune diseases, especially if there’s inflammation present in the digestive tract.

Vitamin B12 is also involved in methylation, which is a reaction that involves moving methyl groups from one carbon chain to another. Many people with autoimmune disease have mutations in their DNA that slow down methylation reactions. This could also lead to lower vitamin B12 levels.

Zinc

Zinc is a very important mineral that supports the immune system and is a potent antioxidant to combat inflammation. Low zinc levels are associated with an increased risk in developing autoimmune diseases and may exacerbate ongoing autoimmune diseases.

How to Know if you Have a Nutrient Deficiency

Here’s how you can investigate whether or not you have a nutrient deficiency:

  • Look for signs and symptoms that correlate to specific deficiencies. Usually vitamin and mineral stores have to be pretty low for symptoms to occur. However, it’s a good place to start.
  • Get tested. I always recommend getting your nutrients tested. Many of them can be ordered through your doctor and be covered by insurance. Vitamin D and a full iron panel are the ones I always recommend getting. B12, folate and homocysteine are also good indicators to uncover any methylation issues.
  • Do a full micronutrient panel with a functional lab. These tests can tell you what your levels are both in and outside of cells. Some people may have normal levels but could have issues with absorption.

How to Reverse a Nutrient Deficiency

If you have an existing nutrient deficiency, supplements are always recommended as food will likely not be enough to replenish your body’s stores. It’s obviously super important to eat a nutrient dense diet, and that should be happening at baseline. But, taking high quality supplements is the best way to reverse a deficiency. In addition, gut healing is also critical at this stage to make sure you are absorbing your supplements. You can take a gut healing supplement that includes glutamine, and/or sip on bone broth to aid the healing process. Lastly, get your vitamin and minerals retested to make sure your interventions are working.

Nutrient deficiencies are common, but they can be easily reversed with the proper diet and supplements. If you would like help navigating this, please contact me to schedule a free discovery call. Feel free to check out my Instagram, Facebook, and YouTube channels for more information about nutrition, lifestyle and autoimmune diseases.

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