How To Heal Gut Flora After Antibiotics



Sometimes you have no choice but to go on antibiotics. You’ve been sick for weeks and you’re not getting better, so you go to the doctor and he confirms what you have been hoping to avoid: ANTIBIOTICS!

Here’s the thing, antibiotics can wreak havoc on your gut flora, but your infection won’t get better until you take those damn pills.

You are caught between a rock and a hard place.


Antibiotics kill off the bacteria responsible for the infection you are targeting. However, they also kill off the good bacteria you DON’T want to touch.

Taking these antibiotics may just give you gas or diarrhea. However, some people may develop more serious issues due to antibiotics, such as:

  • malabsorption
  • Acid Reflux
  • Candida (yeast overgrowth)
  • Acne
  • IBS (irritable Bowel Syndrome)

The good news is you can help your body to stop these issues from occurring, by restoring your gut flora while on antibiotics AND once you are done your antibiotic treatment.

Keep reading to find out how to heal gut flora after antibiotics.

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OK, you’re on antibiotics, but you want to get a jump on restoring your gut flora.

What do you do? Here are a few things you can do.

Being restoring your gut flora by taking a probiotic while you are still on antibiotics. Be sure to take the probiotics 2 hours BEFORE or 2 hours AFTER taking your antibiotic.

Why take within a 2-hour window?

If you take a probiotic too close to taking your antibiotic, the antibiotic will just kill all the good bacteria.

Taking 2 hours before or 2 hours after the antibiotic creates a bit of a buffer. The good bacteria won’t have time to colonize in the gut while you’re on antibiotics, however the good bacteria just passing through will help to keep the opportunistic bacteria in check.



Cut Sugar Out of Your Diet When On Antibiotics

Opportunistic bacteria LOVE sugar. As do Candida, which is a type of yeast. The beneficial (good) bacteria help to keep the yeast and bad bacteria at bay. However, these good bacteria can get killed off and greatly diminished with the use of antibiotics.

As stated before, using a probiotic 2 hours before or after taking your antibiotic, will help. Cutting down or eliminating sugar is another step you can take to lessen the chance of yeast and bacteria overgrowth.

Yeast is a type of fungi that resides in the gut. Antibiotics cannot kill this yeast so this leaves them prone to getting out of control during antibiotic use. Candida is a yeast that can become problematic. Candida thrives on sugar and simple carbohydrates. If there are no beneficial bacteria around to keep the Candida at bay, the yeast will flourish. To keep these fungi from taking over, keep your sugar and carbohydrate intake to a minimum.

Candida won’t get very far if they don’t have a huge sugar food source. Staying away from sugar is always a good idea, but its even more important when you’re taking antibiotics!

After you are done your round of antibiotics, continue to limit your sugar intake. Remember that sugar is not just found in candy and junk food. Carbohydrates like white pasta, bread, rice, and starchy vegetables (potatoes), are all sources of carbohydrates that easily convert to sugar which Candida and opportunistic bacteria LOVE!


Bone Broth

The good bacteria that line your digestive track help to keep the mucus lining intact. This mucus lining keeps the intestinal contents on the inside of the intestines where they belong.

When you are on antibiotics, these bacteria decreases leaving the opportunity for fungi to take root on the intestinal wall. These fungi shoot their roots into the intestinal wall leaving tiny holes. This allows partially digested food particles to seep out of the digestive tract which in turn causes problems.


Hydrolyzed Collagen

Collagen is a protein that holds membranes together. Collagen is found in bone broth or it can be taken in the form of a powder (hydrolyzed collagen) that can be added to other foods or drinks.

Collagen can help to strengthen the wall lining and strengthen the good bacteria that is protecting the intestinal wall.

Taking collagen and/or sipping on bone broth won’t 100% prevent fungi from attaching themselves to the intestinal wall, but it will help to make the good bacteria more resistant to damage and more resilient when the antibiotics are done.



Fermented Foods

Fermented foods contain healthy bacteria such as lactobacilli. These bacteria can help to restore gut microbiota to a healthy balance after antibiotics.


Fermented foods such as sauerkraut, kimchi, keifer and kombucha are some great examples of fermented food to eat after antibiotics.

You can even eat these foods while on antibiotics. Just be sure to follow the same rules as when taking a probiotic while on antibiotics. Eat these fermented foods 2 hours before or after taking your antibiotic. This will allow the good bacteria to kill a few opportunistic bacteria and fungi as they pass through the intestinal tract.



A lot of vegetables are loaded with fiber. Fiber can’t be digested by your body, however it can be digested by your beneficial gut bacteria which will stimulate their growth. This is good as we want as many beneficial bacteria as possible!

High Fibre Foods

Here are some high fiber veggies to start incorporating into your diet once you are done with your antibiotics:

  • Broccoli
  • Brussel Sprouts
  • Sweet Potato
  • Artichoke hearts – cooked
  • Pumpkin

One word of caution regarding Fiber: although it does restore beneficial bacteria after a round of antibiotics, it is best to wait until AFTER you are done your antibiotics treatment before upping your fiber intake.


Well fiber can slow the rate which your stomach empties which will slow the rate at which antibiotics/ medications are absorbed.

Instead, start consuming more fiber after you are done your antibiotic treatment.


We are lucky to be living in an age where we have access to many medicines to help us. However, we need to remember to use these medicines only when absolutely necessary. Overuse of medications like antibiotics can wreak havoc on the gut, which in turn can cause many health issues.

However, when there is no choice and antibiotics must be used, it’s good to have a back-up plan to help keep your gut strong while you are taking antibiotics and to help your gut get balanced after.

I hope this article was helpful. Please see some further studies below for more information on the impact of antibiotics to the gut flora.

10 thoughts on “How To Heal Gut Flora After Antibiotics”

  1. As a pharmacist, I’m always handing out antibiotics to my patients, so I’m very familiar with how they can cause havoc to the digestive system. I’m usually on the ball when it comes to recommending probiotics, but seeing this list has given me some additional, natural, methods I can suggest to patients to further improve their gut health during and after a course of antibiotics.

    I was also intrigued to hear the benefits of cutting out sugar particularly while on antibiotics.

    Thanks for the sharing this, it’s given me some new knowledge which I can now share with patients in the pharmacy 🙂

    • Hi Stephanie, I am glad to pass on information! Yes, sugar is really the worst thing for all of us….yet it’s in everything! The struggle is real! Thank you for taking the time to read this post!


  2. Thank you so much for this extremely helpful article! I recently had a nasty encounter with antibiotics after getting a sinus infection. My flora was screwed up for weeks- I never thought to take probiotics while taking the antibiotics, it was only after and it was already too late that the doctor recommended it. I will definitely keep this in mind next time I need to take antibiotics (hopefully that won’t be any time soon!)

    • Hi Jesse,
      Antibiotics are necessary sometimes, but can do so much damage at the same time! I hope you are on the mend and keep taking those probiotics to boost up those beneficial bacteria! Thanks for taking the time to read this blog post and comment!


  3. Thanks for awesome post! I actually did not know that about antibiotics, but now that I do I know what to expect. I will need to buy some probiotics for sure. Thank you!

    • Hi Jessie,
      You are most welcome! Thank you for taking the time to read and comment. I plan on doing a post in the future about some good probiotic brands.


  4. Hello, great advice and information! I haven’t had a healthy gut in ages. There was an article on how people should take a B complex supplement to get their digestive system back in shape. I take that when I actually remember. Does that sound right to you?

    • Hi Cathy, Yes! B Vitamins can help improve gut health. The best thing to do is to get your diet on track. That is going to be the biggest thing to help with gut health. A per can take a B vitamin supplement, but it won’t do much good if that person’s diet is a mainly processed, high sugar diet. If you need to get your diet on track I HIGHLY recommend the 131 Method book.

      Thank you for your reply and let me know if you have any questions. Feel free to reply or to contact me via email.


  5. Great information that I wished I had a few years back when antibodics caused me problems with digestion and diarrhea. I’ve been on a high fiber diet since 2012 which has controlled some of my problems along with probiotics.

    Which book would you recommend reading first?

    Thanks for the information.

    • Hi Bob, I’m glad this post was informative. I would read Breaking the Vicious Cycle and or Gut and Psychology Syndrome first. These books go into detail about the how and why of the intestines and why they get inflamed and stop working properly. If you do read these books, please feel free to contact me and let me know your thoughts!
      Thanks, Anna


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