How Do I Rebuild My Immune System After Antibiotics?

Published on June 01, 2022

Even the healthiest body encounters challenges every now and then, and occasionally requires a course of antibiotics to treat an infection. 

While they serve a very necessary purpose, you may experience some unwanted side effects of antibiotics, including but not limited to, upsetting your gut health and negative effects on your immune system.

So if you are asking yourself, “How do I maintain a healthy immune system after antibiotics?” you have come to the right place.

In this article, we will discuss how antibiotics impact your body (both positively and negatively) and share four ways to promote healthy immune function after antibiotics.

What Should I Know About Antibiotics?

Antibiotics have become the most commonly prescribed medication by healthcare professionals.

Research has shown that up to 50 percent of antibiotics prescribed are not actually needed or nearly as helpful as predicted. REF#1796 This overuse of antibiotics can lead to what is known as antibiotic resistance. REF#1796

Antibiotic resistance plays a major part in why at least two million people in the United States get serious bacterial infections each year that are resistant to the antibiotics specifically created to threat them. REF#1796

  • At least 23,000 people pass away each year due to an infection that was resistant to antibiotics. REF#1796
  • Almost 250,000 people every year need to be hospitalized due to an infection. REF#1796
  • A minimum of 14,000 people in the United States die each year due to an infection that is resistant to antibiotics. REF#1796

    How Antibiotics Affect Your Body

    A healthy immune system helps fight off invasive bacteria that cause infections (bacterial infections). However, sometimes your body needs a little help. That’s where antibiotics come in.

    Antibiotics are designed to do away with bacteria. They do not treat viruses, but whenfighting off a nasty infection caused by bacteria, they are quite effective, which is good news.*

    Decades ago, people died from infections easily treated today with antibiotics. But what you might not be aware of is that not all bacteria are bad, and in fact, there are some very beneficial bacteria as well. REF#1797

    Bacteria are living microorganisms, some good for your body and others not. REF#1797

    For example, there are two types of bacteria. There are good bacteria in your gut that supports digestion and your immune system.

    Antibiotics typically do a fantastic job of destroying the unwanted, harmful bacteria that cause infection in your body.

    Here is how, according to the Canadian Society of Intestinal Research: “Antibiotics work by disrupting bacterial cells in several ways, such as inhibiting the bacterium’s ability to build its cell wall, blocking its reproduction, or interfering with its ability to store and use energy.” REF#1799

    The problem, however, is that they are also efficient at doing away with healthy gut bacteria in your digestive tract.

    Antibiotics can cause side effects that are directly related to your digestive system

    About one in ten people will have side effects after antibiotic use, such as temporary vomiting, nausea, antibiotic-associated diarrhea, indigestion, and more. REF#1800

    All of that said, it is clear that antibiotic treatment is sometimes necessary.

    Since they can also wipe out the good bacteria in your gut lining, which can impact immune function. After antibiotics you need to care for your digestive tract to sustain your immune system.

    How To Minimize Side Effects While Taking Antibiotics

    If you want to naturally support your body’s ability to handle potential GI-related side effects of antibiotics, you may want to ask your healthcare provider if Saccharomyces boulardii (S. boulardii) is a good option.

    Saccharomyces boulardii is a beneficial yeast that offers probiotic benefits and is often used to help provide relief for GI issues like diarrhea.6 In clinical research, S. boulardii helped to improve diarrhea in children, traveler’s diarrhea, and diarrhea associated with taking antibiotics. REF#1801

    How To Maintain Your Immune System After Antibiotics

    Since much of your immune system depends on your gut bacteria (or microbiome), maintaining your immune system after taking antibiotics is all about supporting your digestive tract function and microbiome health. This will, in turn, support your immune health.

    Because all of your bodily systems are intricately connected, taking care of your body, in general, will also pay off when it comes to maintaining a healthy gut and healthy immune system. 

    That means sleeping well at night, exercising, eating a healthy diet, and managing stress.

    But in addition to those wellness tips, there are a few specific ways that you can care for your gut after a round of antibiotics.

    Eat Fermented Foods or Take Probiotics*

    You may already know this suggestion. Probiotics are beneficial living microorganisms. They can be found in fermented foods (such as those listed below) or taken in supplement form. REF#1802

    When you consume probiotics, these new beneficial microorganisms join the good bacteria you already have in your gut, promoting healthy gut flora.

    To help support your immune system, you can take a high-quality probiotic supplement or increase your intake of the following delicious probiotic-rich foods: REF#1803

    • Yogurt
    • Kefir
    • Kombucha
    • Sauerkraut
    • Pickles
    • Miso
    • Tempeh
    • Kimchi
    • Sourdough bread
    • Some cheeses

    Studies have also shown that probiotics may help with: REF#1804

    • Restoring microbial balance after bouts of diarrhea caused by infections and antibiotics.
    • Helping to support and maintain GI tract health and regularity.
    • Supporting the immune system by supporting immune defense in the gut.

    Take Prebiotics

    We just talked about probiotics. Now we are going to talk about prebiotics.

    What’s the difference? 

    Prebiotics are fiber that nourishes your gut bacteria (probiotics). In other words, prebiotics are what the microorganisms in your gut feed on. Without prebiotics, the good bacteria in your gut can not flourish. REF#1805

    Some prebiotic foods to try include: REF#1805

    • Asparagus
    • Beets
    • Garlic
    • Onion
    • Jerusalem artichokes
    • Wheat
    • Honey
    • Bananas
    • Barley
    • Lentils
    • Tomatoes
    • Rye
    • Soy
    • Milk
    • Peas
    • Beans
    • And more

    Unfortunately, prebiotics are present in these foods only in low concentrations. That’s where prebiotic supplements come in.

    Gaia Herbs Microbiome Food is a plant-based prebiotic powder for digestive health made with beneficial herbs, including Larch, Acacia, Acerola, Fenugreek, Cinnamon, and Ginger.*

    With no added fillers, flavors, or sweeteners, you can feel good about what you are putting in your body.

    This powder is convenient to use and mixes easily in water. 

    Adults should mix one teaspoon into four to six ounces of water and drink it daily between meals. You can gradually increase to one tablespoon per day for additional prebiotic support.*

    Support a Calm Stomach*

    When good bacteria are wiped out because of antibiotics, in addition to supporting the population of beneficial microorganisms, you also want to aid digestion and soothe your stomach. 

    After all, it may not be at its best without those beneficial bugs.

    Turn to Gaia Herbs’ Microbiome Cleanse to help support a healthy GI tract.

    This formula is made with Black Walnut and Peppermint oil to help your digestion when there are changes in your routine (like taking antibiotics). 

    Support Digestion and Natural Cleansing*

    If you’re looking for an Ayurvedic go-to to support regularity and gently cleanse your system, consider Triphala Fruit. Ours is a vegan capsule made with a three-fruit blend consisting of Amla, Belleric Myrobalan, and Chebulic Myrobalan.

    To take advantage of the benefits of Triphala Fruit, simply take one capsule two times a day between meals.*

    Discover Daily Immune Support*

    Now that we’ve talked about four ways to maintain a healthy immune system and improve your overall health after taking antibiotics, we want to leave you with some natural options for immune support.*

    We recommend Astragalus Root and Traditional Mushrooms, found in the following immune-support products.*

    Everyday Immune Mushrooms & Herbs

    Gaia Herbs Everyday Immune Mushrooms & Herbs contains a blend of organically grown mushrooms (including Chaga, Cordyceps, Maitake, and Reishi) and herbs designed to help sustain overall wellness.*

    Adults should take one capsule twice a day and continue to use it long-term for the best results.*

    Immune Mushroom Blend

    For more year-round immune support from mushrooms, turn to our Immune Mushroom Blend, a mix of five potent immune mushrooms—Reishi, Cordyceps, Turkey Tail, Shiitake, and Chaga

    The mushrooms are organically grown and sustainably sourced. At 5x strength, you only need one capsule per day.*

    Immune Shine™

    If you prefer a powder you can mix into smoothies or drinks, Gaia Herbs Immune Shine™ is a great option. 

    This USDA Certified Organic powder combines all the benefits of mushrooms that support immune health with herbs traditionally used to maintain overall well-being.

    To benefit from the Astragalus, Maitake, Chaga, Black Elderberry, and Ginger in this supplement, simply mix one teaspoon of powder into a smoothie, dairy or non-dairy milk, or any other beverage of your choice and enjoy.*

    One last tip for the busy and stressed-out among us: Stress can tax the immune system over time, especially when it may be affected after a round of antibiotics.

    For long-term immune support during stressful times, turn to Eleuthero and Ashwagandha.

    These adaptogenic herbs can help your body cope with stress in a healthy way so you can stay feeling your best.*

    Gaia Herbs offer many options for supporting a healthy immune system.* You can browse them here.

    Probiotics and Prebiotics to Help Sustain Immune Health*

    Antibiotics are a modern medical marvel that has saved millions of lives. 

    The downside is that in addition to killing the bad, unwanted bacteria, antibiotics can also damage your good gut bacteria.

    To maintain your immune system after antibiotics, you’ll want to take good care of your digestive system.

    A healthy gut is essential to a healthy immune system. With just a bit of extra care, you can support your gut microbiome to help maintain your immune system during and after antibiotics.


        • 1. Cleveland Clinic, "Antibiotics: Side Effects, What Is It & Usage", n.d..
        • 2. Mary Cheung, MD,, "6 Things You Should Know About Your Gut Bacteria", The Well by Northwell, accessed April 18, 2021..
        • 3. , "All About Antibiotics", GI Society, accessed April 18, 2021.
        • 4. Huizen, Jennifer, "What Are the Side Effects of Antibiotics?", December 17, 2021.
        • 5. Pais, P., Almeida, V., Yılmaz, M., & Teixeira, M. C. (2020), "Saccharomyces boulardii: What Makes It Tick as Successful Probiotic?", Journal of fungi (Basel, Switzerland), 6(2), 78.
        • 6. NCCIH, "Probiotics: What You Need To Know", n.d..
        • 7. , "How to Get More Probiotics", Harvard Health Publishing, Harvard Medical School, updated August 24, 2020.
        • 8. RDN, Allyn Wergin, "An Introduction to Probiotics", Mayo Clinic Health System, July 13, 2022.
        • 9. DNP, Amanda Gingrasso, "Good Bacteria for Your Gut", Mayo Clinic Health System, April 1, 2022.