grab my *free* Starter Kit:

3 daily habits that improve
leaky gut and autoimmunity!

How to Recover from Antibiotics + Restore Your Gut Microbiome

Filed Under:

Antibiotics serve as an essential part of medical treatment. But, it’s important to protect your gut during and after any antibiotic protocol. Implement these lifestyle and diet practices to protect your microbiome and recover from antibiotics.

how to recover from antibiotics

Reading Time: 8 minutes

Antibiotics have grown to be an effective and common treatment for many infections and diseases in America today. While they are proven to be beneficial against bacterial infections, specifically, antibiotic use does not come without its risks and side effects. In circumstances when antibiotics are a necessary method of treatment, it’s important to know how to protect your health and mitigate any short-term and long-term side effects or consequences.


According to the Microbiology Society, antibiotics are a “type of antimicrobial designed to target bacterial infections within (or on) the body.” Simply speaking, antibiotics essentially stops the growth of bacteria in the body and prevents it from spreading through your bloodstream, which can lead to septic shock. Antibiotics are specifically beneficial when bacterial infections are present in the body, such as strep throat or H. Pylori in the gut. Fun fact: around 1950, when antibiotics were used to treat fatal conditions, the average human life expectancy increased by 8 years. Needless to say, antibiotics serve an important purpose, and can be life saving in certain situations! 

do i really need antibiotics

That said, there is an appropriate time and place for antibiotic use. Trouble arises when antibiotics are used excessively or without appropriate cause. For example, using antibiotics in unwarranted circumstances, such as treatment for a viral infection, can lead to antibiotic resistance. In other words, the more you utilize an antibiotic protocol, the more likely the gut will remember and recognize the antibiotic, eventually making it ineffective at killing the infection. Antibiotic resistance commonly occurs when antibiotic protocols are used for viral infections or when protocols are started, but not finished through.

In addition to antibiotic resistance, overuse of antibiotics has damaging effects on the gut and microbiome. While antibiotics are effective at killing pathogenic bacteria in the body, they cannot discriminate between beneficial and harmful bacteria. Hence, antibiotics also kill off the beneficial bacteria in your body. This can lead to a bacterial imbalance, such as dysbiosis, and eventually cause leaky gut and/or autoimmunity. This disruption in the gut microbiome has also been shown to increase the risk of depression.

As you can see, antibiotics are a powerful tool. When used appropriately, they can be a life-saving treatment. However, in inappropriate situations, they can cause more harm than good.


If you’ve been prescribed multiple antibiotic protocols in your lifetime, or worse, within the last few years, you might be dealing with the consequences of antibiotic overuse. Unfortunately, using antibiotics repeatedly or improperly, can lead to a host of symptoms, often gut-related, such as:

  • Autoimmunity
  • Allergies and/or asthma
  • Diarrhea
  • Depression and/or anxiety
  • Skin problems
  • Weight gain
  • Yeast infections

If you suspect you might be dealing with the aftermath of antibiotic overuse, it’s important to learn how to effectively recover from antibiotics.

symptoms of antibiotic overuse

Antibiotics serve as an effective approach to bacterial infections and diseases and are often an essential part of medical treatment. But, it’s important to protect your gut microbiome during and after any antibiotic protocol. Protecting the gut microbiome not only prevents antibiotic-related side effects, but also reduces the risk of gut dysbiosis. Implement these lifestyle and diet practices to protect your gut microbiome during and after a course of antibiotics.

how to recover from antibiotics
Focus on Quality Foods

The months after taking antibiotics is no time to skimp on quality. This would be the most crucial time to give your gut a break from irritants and common triggers and give it the quality whole foods it needs to replenish and restore. This means choosing organic produce as much as possible and limiting packaged foods whenever possible. 

Choosing a variety of organic fruits, vegetables, pasture-raised meats, grass-fed beef, raw A2 dairy, grass fed butter and animal fats, and wild caught fish should be the center of your diet for the months following an antibiotic protocol. Idealls, following an anti-inflammatory diet for at least 6 months post antibiotics is best! 

Eliminate Sugar and Processed Foods

Pathogenic bacteria and yeast in the body feed on sugar. Hence, consuming high-sugar foods and drinks only increases pathogenic bacteria in the body. While eating a high-sugar diet is never considered to be “healthy,” it can be especially damaging during a course of antibiotics, as the body is already vulnerable to bacterial imbalances. During and after antibiotic treatment, consume a low-sugar diet to prevent an overgrowth of pathogenic bacteria and yeast.

Sip on Bone Broth 

Bone broth is a nutritional powerhouse for the gut! It is rich in minerals, glutathione, glutathione, and gelatin. These nutrients can help support the gut after antibiotic treatment and speed up recovery. You can easily make your own bone broth at home or buy it premade from a quality brand such as Fond

To learn even more about the health benefits of bone broth beyond antibiotics, check out this post here

Take Extra Probiotic Supplements

Probiotic supplementation reduces the risk of antibiotic-associated diarrhea and helps to re-establish balance in the gut microbiome. If you’ve recently completed a functional gut test, it is especially important to supplement with the specific probiotic strains recommended to you by your provider. This is arguably the most effective approach to protecting your gut microbiome during antibiotic treatment. 

Typically during antibiotics you’ll want to choose a probiotic with a high number of colony forming bacteria (above 100 billion probiotics and multi strain). For most of my clients, I choose ProBio Med by Designs for Health or Ortho Biotic 225 by Ortho Molecular Labs (my personal go to). These options are packed with enough beneficial bacteria to help support the microbiome during antibiotic use and can help minimize stomach discomfort. 

However, if your gut has not been tested recently after antibiotics, I recommend supplementing with Seed, a scientifically-backed probiotic + prebiotic capsule with 24 clinically-studied strains. Another great option is MegaSpore Biotic by Microbiome Labs. This is available through searching the catalog on Fullscript. In general, probiotics should be taken for at least 6 months during and post antibiotics (at least) to support and recolonize the microbiome. 

Consider Drinking Kombucha

Kombucha is a fermented tea. During the fermentation process, microorganisms (ie. bacteria and yeast) work to convert carbohydrates into organic acids and alcohol, resulting in a delicious drink that is naturally rich in probiotics. When looking for a high quality kombucha, check the ingredient list to make sure there are no added sugars. It’s also important to look for organic ingredients. Aim to drink 8 ounces of kombucha, daily.

Reduce Inflammation 

Antibiotics are known to irritate the lining of the gut and can even destroy villi that lines the small intestine. This inflammation can set the stage for intestinal permeability and even further imbalances such as food sensitivities and gut infections. To support inflammation along the gut lining, consider adding more anti-inflammatory foods, herbs, and spices into your diet. 

Garlic and ginger are both helpful for reducing inflammation and can help speed up recovery. You can add both garlic and ginger to foods, smoothies, juices, and teas. In addition, specific herbs and even certain herbal teas are known to soothe an irritated gut lining and support the overall inflammation in the body. 

Incorporate Fermented Foods 

Fermented foods, similar to kombucha, contain naturally-occurring probiotics. Common fermented foods include kimchi, sauerkraut,  raw dairy, and kefir. To confirm a fermented food is optimally beneficial to the gut, look for a label verifying it contains ‘live cultures.” If possible, opt for an unpasteurized option, as pasteurization kills off some of the beneficial probiotic organisms and reduces its effectiveness.

Eat More Fiber 

Fiber is an excellent source of prebiotics. Prebiotics are essentially food for probiotics. They are responsible for feeding the beneficial bacteria in the gut. Prebiotics release short chain fatty acids (SCFAs), which helps to reduce inflammation in the body. More importantly, they modulate the immune system and gut.

Here’s 9 of the best prebiotics you can add into your diet to support your gut after antibiotics.

Include Immune Supporting Foods

The immune system is located in the gut so it shouldn’t come as a surprise that we need to support the immune system if we want to help restore our gut after antibiotics. The best immune supporting foods are going to be foods high in both vitamin A and vitamin C. The combination of these water soluble vitamins have a synergistic effect on the immune system. Choose orange colored foods such as squash, pumpkin, sweet potato, cantaloupe for vitamin A and antioxidants along with good quality beef liver. For vitamin C, choose fruits such as kiwi, pineapple, strawberries, apples, and oranges along with vegetables such as broccoli, leafy greens, cabbage, potatoes, and peppers. 

In addition, adding superfood powders that are concentrated and high in food based vitamin C can be really effective since it is not always easy to get enough of these foods above through diet alone to support a weak immune system. I love Earthly Immune aid for this

You can also find organic camu camu powder or acerola cherry powder at your local health food store and add it into your smoothies for a vitamin C boost.

recover after using antibiotics

Supplementation is best when customized based on your unique chemistry, however there are certain nutrients that can be beneficial for just about anyone looking to restore their gut health after taking antibiotics. Talk to your practitioner about some of these options and if they are right for you! 





Aloe Vera 

Beef Liver Capsules

Camu Camu Vitamin C 


There are many factors that will play a role in gut recovery after taking antibiotics. This is going to vary based on the specific antibiotic protocol someone is on, the length of time on the antibiotics, and the overall health (especially gut health) of the person on antibiotics. 

For this reason, now is always the time to prioritize gut health! Whether you are currently taking antibiotics, just finished antibiotics, or looking to prevent having to go on antibiotics again, prioritizing your gut health today should be a priority. 

Here are the 5 reasons gut health is so important.


When antibiotics are used appropriately, they can be a life-saving treatment. However, in inappropriate situations, they can cause more harm than good.

My personal stance on antibiotics is that it’s best to try really hard to avoid them. In the situations where they are highly recommended and can be life saving, it might be worth the risks. 

If you’ve taken multiple courses of antibiotics throughout your life and suspect your gut bacteria is out of whack as a result, it’s time to get tested. Working with a functional medicine practitioner who focuses on gut health is the best way to identify any imbalances or infections and achieve long-term healing. This is exactly what I help my clients achieve inside my personalized Microbiome Makeover program! 

How to Recover and Restore the Gut After Antibiotics

Leave a Reply

Your email address will not be published. Required fields are marked *

"When it comes to balancing our body, healing the gut, reversing autoimmunity, and achieving optimal health—we are a lot like a car that won’t run right. In order to fix the problem once and for all instead of relying on jumper cables, we must get underneath the hood, run the diagnostics, and replace the battery so that it runs good as new."

-Nikki Yelton, RD

a note from nikki:

If you are ready to stop wasting precious time, get off the never-ending hamster wheel, and finally surrender trying to figure things out on your own—this is your moment. 

You don’t have to settle for just getting by and hoping tomorrow is a better day. We both know you are a woman who deserves better and are made for so. much. more.

are you ready?

Ready to resolve your GI distress, reverse autoimmunity, and live your extraordinary life?

I believe every woman can take back their health!

hey there!