You’re eating healthy, taking supplements, and doing your best—so why do you still feel exhausted, foggy, and inflamed?

For many women living with autoimmune conditions, the answer lies in what your body isn’t absorbing—even when you’re doing everything “right.”

Micronutrient deficiencies are a global health issue, but they hit even harder when you're dealing with autoimmune disease. These hidden deficiencies can worsen inflammation, pain, and other debilitating symptoms, making it feel like true relief is always out of reach.

More than 5 billion people worldwide aren’t consuming enough of key nutrients like iodine, vitamin E, and calcium. And for those with autoimmune conditions, poor gut health can block even the best nutrients from being absorbed.

In this post, we’ll explore:

• The most common deficiencies that worsen autoimmune symptoms

• What stops your body from absorbing nutrients in the first place

• Functional tests that can help uncover what your body is really missing

• How to support absorption so you can finally feel better

Top Micronutrient Deficiencies and Their Impact on Autoimmune Health

Iodine

Essential for thyroid health and hormone balance—especially important in Hashimoto’s and other thyroid-driven autoimmune conditions.

• Food Sources: Seaweed, iodized salt, dairy, fish

• Supplement Tip: Use caution; too much can cause thyroid flare-ups.

Vitamin E

A powerful antioxidant that helps calm inflammation, support immune balance, and reduce oxidative stress.

• Food Sources: Sunflower seeds, almonds, spinach, avocados

• Supplement Tip: Look for d-alpha-tocopherol for better absorption. Liquid or oil-based supplements may benefit individuals with absorption issues.

Calcium

Supports bone health, nerve function, muscle contraction. Poor gut health can make it harder to absorb.

• Food Sources: Leafy greens, sesame seeds, high-quality dairy

• Supplement Tip: Smaller doses throughout the day are easier to absorb and reduce risks associated with excessive intake.

Iron

Low levels are extremely common in autoimmune conditions, leading to fatigue and poor immune function.

• Food Sources: Red meat, lentils, spinach

• Supplement Tip: Iron bisglycinate is gentle on the stomach and well absorbed. Pairing with vitamin C-rich foods improves absorption.

Folate (Vitamin B9)

Important for detox, energy, and nervous system support.

• Food Sources: Spinach, lentils, asparagus, citrus

• Supplement Tip: Choose methylfolate if you have MTHFR or gut absorption issues.

Vitamin C

Supports tissue repair and immune defense—and helps your body absorb other nutrients like iron.

• Food Sources: Citrus fruits, bell peppers, broccoli

• Supplement Tip: Ascorbic acid is effective, though buffered vitamin C may be gentler on the stomach.

Autoimmune Disease and Nutrient Absorption: Why Gut Health Matters

Even if your diet is full of nutrient-rich foods, your body might still be starved for key vitamins and minerals if your gut isn’t absorbing them well.

What Impairs Nutrient Absorption in Autoimmune Conditions?

Chronic Inflammation
Autoimmune conditions like Crohn’s, celiac disease, and ulcerative colitis damage the gut lining, reducing absorption of iron, folate, and fat-soluble vitamins (A, D, E, K). Even non-GI autoimmune conditions like lupus and rheumatoid arthritis can impair digestion systemically.

Low Stomach Acid
Common in autoimmune patients, this interferes with the breakdown of proteins and the absorption of nutrients like B12, magnesium, calcium, and iron. Causes include chronic stress, aging, and long-term use of acid-blocking medications (such as PPIs for GERD or NSAIDs for pain management). Without sufficient acid, food particles remain undigested, leading to bloating, nutrient deficiencies, and bacterial overgrowth in the small intestine (SIBO).

Leaky Gut (Increased Intestinal Permeability)
When the gut lining becomes compromised, undigested particles and toxins leak into the bloodstream, triggering immune flare-ups and blocking absorption. Nutrients most affected include zinc, iron, and B vitamins.

Gut Dysbiosis (Microbial Imbalance)
An unhealthy gut microbiome leads to bloating, malabsorption, and nutrient depletion. Overgrowth of harmful bacteria or yeast (like Candida) is common in autoimmune conditions and makes everything harder—from digestion to energy production.

How to Optimize Nutrient Absorption When You Have Autoimmune Disease

You can’t heal what your body can’t absorb. Here are powerful, practical steps to help your body take in the nutrients it desperately needs:

• Remove inflammatory foods: Limit gluten, dairy, sugar, and processed foods that irritate the gut lining.

• Aid digestion: Consider digestive enzymes, apple cider vinegar, or HCl supplements (with professional guidance) to help break down food and help nutrient uptake.

• Heal the gut lining: Add collagen, bone broth, and L-glutamine to support tissue repair and reduce permeability.

• Rebuild your microbiome: Include probiotics and prebiotic foods like yogurt, kefir, sauerkraut, and garlic.

• Diversify your plate: Eat a wide range of colorful, whole, anti-inflammatory foods rich in essential vitamins and minerals that nourish your body and gut.

• Manage stress: Chronic stress damages the gut lining and slows digestion. Use mindfulness, breathwork, or gentle movement to help regulate.

• Address root causes: Work with a functional medicine provider to explore underlying issues like leaky gut, SIBO, infections, or hormonal imbalances.

Functional Testing for Micronutrient Levels

If you’ve ever been told “your labs are normal” but still feel terrible—functional testing can reveal what’s really going on under the surface.

These common functional tests help identify hidden deficiencies and uncover the why behind your symptoms so you can move forward with clarity.

1. Blood Tests
Can measure levels of specific nutrients like vitamin D, B12, iron, and folate. A great first step to guide your nutrition or supplement plan.

2. Comprehensive Metabolic Panel (CMP)
Assesses electrolytes, kidney and liver function, and protein levels. It gives you a bigger picture of how well your body is functioning—and can reveal signs of malnutrition or deficiency.

3. Advanced Micronutrient Testing
Specialized labs offer intracellular and extracellular micronutrient testing for a full view of vitamin, mineral, and antioxidant levels. These tests help tailor interventions to your body’s needs.

4. Organic Acids Test (OAT)
This urine test looks at metabolic byproducts that reveal deficiencies in B vitamins, amino acids, and fatty acids—often missed in standard labs. It’s especially helpful for patients with energy issues, brain fog, or chronic fatigue.

5. Comprehensive Stool Testing
Since so much of nutrient absorption happens in the gut, stool tests can uncover infections, inflammation, poor digestion, or microbiome imbalances that block your body from getting what it needs.

You Don’t Have to Keep Guessing

Micronutrient deficiencies don’t just cause fatigue and brain fog—they keep you stuck in survival mode. And when your gut isn’t working properly, even the cleanest diet won’t be enough.

But with the right support and testing, you can uncover what your body truly needs and build a plan that works.

If you’re ready to feel like yourself again, let’s talk. You don’t have to keep pushing through—there’s a way forward, and it starts with real answers.

Sources

Passarelli, Simone et al. "Global estimation of dietary micronutrient inadequacies: a modelling analysis." The Lancet Global Health, Volume 12, Issue 10, e1590 - e1599.

World Health Organization. "Vitamin and Mineral Deficiency (VMD)." WHO.

De Benoist, Benedicte et al. "Iodine Status Worldwide: WHO Global Database on Iodine Deficiency." World Health Organization, 2004.

"Dietary Reference Intakes for Calcium and Vitamin D." Institute of Medicine, 2011.

"Iron Deficiency Anemia." Centers for Disease Control and Prevention, 2021.

"Vitamin E: Fact Sheet for Health Professionals." National Institutes of Health, 2021.

"Folate." National Institutes of Health, 2021.

"Vitamin B12 Fact Sheet for Health Professionals." National Institutes of Health, 2021.

"The Role of Gut Microbiota in Nutrition and Health." Nature Reviews Gastroenterology & Hepatology, 2020.

"Nutritional Deficiencies and Their Role in Health and Disease." Journal of Nutrition and Metabolism, 2019.