We all know that a balanced, anti-inflammatory, nutrient-dense diet, such as AIP, paired with consistent, supportive lifestyle habits, plays a key role in successfully managing autoimmune disease. As a practitioner, I’m also a firm believer in the power of therapeutic nutrients, often referred to as nutraceuticals.
In this article, I highlight my top five nutraceutical (supplement) recommendations for supporting and balancing our immune system while navigating an autoimmune diagnosis. Let’s dive in!
A quick recap on Autoimmunity
Autoimmune disease occurs when the immune system, designed to protect us, begins mistakenly attacking our own tissues. Instead of recognizing “self” from “non-self,” the immune system becomes confused and launches inflammatory responses in places it shouldn’t.
While symptoms differ from one condition to another, the underlying mechanism typically involves loss of immune tolerance and an overactive immune response that struggles to shut off an attack once it begins.
One way to understand this is through the balance between different types of immune cells, often referred to as T-helper (TH) cells, which coordinate immune activity. Here’s a simple way to think about it:
The TH1 / TH2 Imbalance — A Simple Analogy
Imagine your immune system as a seesaw:
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TH1 cells handle the “search and destroy” side of immunity, fighting viruses, removing infected cells, and clearing threats.
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TH2 cells drive the “antibody-making” side, which helps mount a response to allergens and parasites.
In a healthy immune system, these sides work in harmony. But in autoimmunity, one side can become dominant, leading to a lopsided response, like a seesaw stuck on one side. Some people are TH1-dominant, others TH2-dominant, and symptoms or triggers may differ depending on which side is more active.
A significant note:
Some functional medicine practitioners may use supplements to shift TH1 or TH2 dominance intentionally. This should never be done without professional guidance. Manipulating immune pathways on your own can trigger a flare or worsen symptoms.
TH3 Cells: The “Regulators” We Want More Of
While TH1 and TH2 drive immune responses, TH3 cells act as the brakes. They help regulate inflammation, maintain immune tolerance, and prevent overreaction.
Supporting TH3 activity rather than pushing TH1 or TH2 is often a safer, more effective way to promote balance and resilience in the immune system.
This is where targeted supplementation, paired with a nutrient-dense AIP lifestyle, can be incredibly helpful.
Below are five supplements that naturally support immune balance and regulatory pathways.
1. Fat-Soluble Vitamins (A, D, E, K)
Fat-soluble vitamins play essential roles in immune modulation, tissue repair, barrier integrity, and the control of inflammation.
How They Help:
- Vitamin A: Supports mucosal immunity and immune tolerance.
- Vitamin E: Acts as an antioxidant to reduce inflammation.
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Vitamin K: Works synergistically with vitamin D for bone and immune health.
Vitamin D deserves special emphasis.
Vitamin D is one of the most powerful immune-modulating nutrients we have. It directly influences regulatory immune cells (including TH3) and helps maintain immune tolerance.
Optimal levels for autoimmunity are often between 70–100 ng/mL, though your provider should help determine your target range.
Liquid vitamin D is often easiest to absorb, especially for individuals with digestive or absorption challenges.
2. Glutathione (Topical or Liposomal)
Glutathione is your body’s master antioxidant and a critical player in detoxification, mitochondrial health, and inflammation reduction.
Why it matters for autoimmunity:
- Neutralizes oxidative stress that drives autoimmune flares
- Supports liver detox pathways
- Helps regulate immune response
Important: Oral glutathione is poorly absorbed. Look for liposomal or topical forms for therapeutic benefit.
3. Probiotics
Your gut houses over 70% of your immune system, so supporting microbial diversity is one of the most powerful ways to promote immune balance.
Benefits include:
- Strengthening the gut barrier
- Enhancing regulatory immune responses
- Reducing inflammation
- Supporting production of short-chain fatty acids (more on that next!)
The goal is not just “more bacteria,” but the right balance of beneficial strains.
4. EPA & DHA (Omega-3 Fatty Acids)
These anti-inflammatory fatty acids support brain health, cardiovascular health, and, critically, immune regulation.
For autoimmunity, EPA & DHA help:
- Reduce inflammatory cytokines
- Support cellular repair
- Promote regulatory immune activity
- Improve the fatty acid balance that influences immune signaling
A general therapeutic range is 3–4 grams per day, but always check with your doctor first if you have contraindications (such as clotting disorders or certain medications).
5. Short-Chain Fatty Acids (SCFAs)
SCFAs, like butyrate, are produced when beneficial gut bacteria ferment dietary fibers. They play a significant role in immune regulation.
SCFAs help:
- Reduce intestinal inflammation
- Strengthen gut barrier integrity
- Promote T-regulatory (TH3) activity
- Support a balanced immune response
Even with a nutrient-dense AIP diet, supplementation can help if gut diversity is low or digestion is compromised.
Safe Supplementation: Work With a Professional
Autoimmune disease is complex, and supplement strategies should be tailored to your unique biochemistry, triggers, and health history.
While these supplements can support immune balance, they should not replace professional guidance, especially for those with multiple autoimmune conditions, significant inflammation, or a history of flares.
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Final Thoughts
Autoimmune healing isn’t about suppressing your immune system; it’s about helping it regulate itself again. By supporting regulatory pathways (TH3), strengthening the gut-immune connection, and filling in key nutrient gaps, you can help your body find more balance, stability, and resilience.
Happy Healing!