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Best Alternatives to Immunosuppressants

June 22, 2026 by Dr. Tiffany Caplan, DC, CFMP, IFMCP & Dr. Brent Caplan, DC, CFMP, IFMCP

Alternatives to Immunosuppressant Drugs in Autoimmune Disease 

Many people with autoimmune disease are prescribed immunosuppressant medications. However, these drugs are linked to many side effects. Immunosuppressant drugs’ side effects include a higher risk of infections, unhealthy blood sugar, weight gain, bone loss, hormone imbalance, or mood issues, depending on which autoimmune disease medication is used. Because their job is to suppress the immune system, immunosuppressant drugs can leave a person defenseless against the outside world. As a result, people are often searching for natural alternatives to immunosuppressants.

Before we dive into the concept of natural immunosuppressants, I want to point out that I’m not anti-medication. There is a time and a place for medication management. I have even referred people out for medication management when I believe that medication is going to get them better faster or get them to a place where they’re well enough to do the work to address the root causes of their autoimmune disease. Some people are in such a bad place that they need some pain management to be able to put in the work to make dietary or lifestyle changes. 

I don’t think there’s anything wrong with medication management of autoimmune disease if it’s being used as a tool with the intention of doing more work to fix the root problem instead of just relying on the medication forever as the fix.

Having said that, whenever possible, functional medicine uses alternatives to immunosuppressant drugs. In this blog post, I’ll dive into the reasons why suppressing the immune system isn’t a great idea and what you can do instead to heal autoimmune disease. 

What Are Immunosuppressant Drugs?

Immunosuppressant medications lower immune system function to stop it from attacking healthy cells and tissues. If you have an autoimmune disease, conventional doctors usually prescribe these type of drugs. Immunosuppressant drugs for rheumatoid arthritis, ulcerative colitis, Crohn’s, and other autoimmune diseases may include:

  • Prednisone (corticosteroids)
  • Humira or Enbrel (biologics)
  • Protopic (calcineurin inhibitors)
  • CellCept (inosine monophosphate dehydrogenase [IMDH] inhibitors)
  • Xeljanz (Janus kinase inhibitors)
  • Rapamune (mechanistic target of rapamycin [mTOR] inhibitors)

Although conventional medicine relies heavily on immunosuppressant medications, functional medicine takes a different approach. 

Suppressing the Immune System Is Not the Solution

The conventional medicine approach focuses on the overactive immune system, which is causing damage in the body. So, they want to stop it from doing that. The goal is to suppress those parts of the immune system that are overactive, or generally suppress the immune system’s function, to stop the damage and relieve the symptoms. 

In functional medicine, we’re not trying to suppress the immune system. We’re trying to modulate the immune system. We don’t want to just suppress a system that’s supposed to be working in your body. We want to understand why it’s out of balance and help support it back into balance. The immune system is like your check-engine light coming on. It’s your body’s way of trying to get your attention that there’s something not working well here and it’s confusing the immune system, causing it to make mistakes. And so instead of just trying to shut the immune system down, we have to figure out what’s causing it to make mistakes.

Natural Immunomodulators

The goal is not what we call green pharmacy, where instead of a pharmaceutical suppressing the immune system, we’re going to use herbs to suppress the immune system. That’s not at all what we’re trying to accomplish. We’re trying to modulate the immune system rather than bullying it into shutting down. That’s why we use immune modulators, which calm the overactive parts of the immune system and support the weaker parts. Immune modulators include:

• Omega-3 fatty acids

• Vitamin D3

• Curcumin

• Resveratrol

• Glutathione

• Other antioxidants

We’re trying to get the immune system back into balance so it will respond properly. Immunomodulators help do that. However, the important part is understanding why the immune system is in in such an imbalanced state to begin with. We want to help remove the factors that are triggering it to act that way. If there’s a part of the immune system that’s upregulated, what are the factors that are keeping it in that high alert state?

Natural immunomodulator supplements are not the only tool. Diet, nutrition, and lifestyle changes can modulate the immune system. Those factors highly influence how the immune system works and what parts of it are being turned on or stimulated and which parts are being suppressed or calmed down.

Gut Bacteria as a Natural Immune Modulator

The gut is host to microbes that highly influence our immune system activity. The wrong organisms or pathogens produce toxins. They create inflammatory responses that are going to trigger the immune system. On the flip side of that, the good bacteria in the gut are really helpful for the immune system, especially because they help with factors like short-chain fatty acid production. And the short-chain fatty acids keep the gut barrier intact, protecting the immune system from overexposure to pathogens. 

The Two Sides of Immunity

Our goal in using immune modulators is to address two sides of the immune system. When the immune system is out of balance, part of it is going to be overactive. But there are also parts of the immune system that are underactive. The cells that regulate these two parts of the immune system and keep them in balance are called regulatory T cells (Treg cells). Many immune modulators help Treg cells to work properly.

Other Factors That Impact Immunity

Since the goal is to find out why your immune system is imbalanced rather than suppressing it, we need to look at potential causes of autoimmune disease, as well as factors that make your autoimmune disease worse. I talk with my patients about these nine root causes of autoimmune disease, which can help turn around autoimmune conditions once they are properly addressed. 

We need to look for environmental triggers including seasonal allergies, which impact the immune system. Other environmental factors that trigger the immune system include exposure to toxins, chemicals, and mold.  

When we think about natural immunomodulators, we need to consider our lifestyle habits, the choices we make, and our environmental exposures instead of just asking, “What vitamins can we take?” Supplements can be good tools and they can help with modulating the immune system, but ultimately what is going to modulate the immune system most effectively is removing or avoiding the triggers that have the immune system so upset in the first place.

If you identify what’s triggering your overactive immune system and take action to reduce or eliminate those triggers, it puts you back in the driver’s seat of your health. Once you understand what your body likes or dislikes, you can make more informed choices about how to take care of your body. A lot of people with autoimmune disease start out with a conventional medicine understanding of it: the immune system is just overactive. Likewise, they believe it makes sense to suppress it. But in reality, we need to regain control over the immune system. We need to help get it back into a balanced state. We need to find out why this autoimmune dysfunction is happening in the first place. 

Taking Control of the Immune System with Functional Medicine

You can find out why your immune system is out of balance when you work with a functional medicine provider. Here at the Caplan Health Institute, we can pinpoint the triggers and causes of your autoimmune imbalance. The first step is to schedule a free 15-minute discovery consultation, by phone or video. 

If you decide to come on board as a practice member, we can order tests and create a personalized plan to get your immune system back in balance. We call our patients “practice members” because they take an active role in their health.  

We can suggest alternatives to immunosuppressant drugs in order to modulate your immune system rather than shut it down. By balancing your immune system, we can reduce or eliminate your autoimmune symptoms over the long-term. You’ll have more energy, feel like your old self again, and be able to do the things you love to do. 

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