How to Restore Your Child's Gut After Antibiotics
If you’ve landed here, chances are your child has recently taken antibiotics—and now you’re wondering how to support their gut health and get things back on track.
You’re not alone. Many parents feel unsure, even a little anxious, about how antibiotics might affect their child’s digestion, immunity, and overall well-being. I’ve been there, too—not just as a nutrition professional trained in gut health, but as a mom who wants to do everything she can to nurture a healthy foundation for my children.
The good news? Children’s bodies are incredibly resilient, and with the right foods, habits, and simple strategies, you can help their gut microbiome recover and thrive.
Let’s walk through exactly how to do that—without the overwhelm. In this article, we’ll cover how antibiotics can affect gut health, natural ways to restore gut health after antibiotics (like eating prebiotic and fermented foods and avoiding those that fuel bad bacteria), and how to effectively incorporate probiotics to help rebuild the microbiome.
photo credit: Alexander Dummer
How antibiotics can affect gut health
The first three years of life are a critical period for microbiome and gut health development. It also happens to be a time when ear infections and other illnesses are most common. In fact, ear infections are one of the top reasons antibiotics are prescribed.
Antibiotics can be lifesaving, and I’m grateful we have access to them when truly needed. But knowing how to support your child’s body during and after a course can have lasting benefits for their health (and everything here applies to adults, too!).
Antibiotic use, especially in the first year of life, has been shown to reduce the diversity of the gut microbiome and is correlated with increased risk of conditions like atopic dermatitis. It’s associated with a drop in beneficial bacteria like Bifidobacterium and Lactobacillus, and a rise in less-beneficial bacteria like E. coli.
Because about 80% of the immune system is based in the gut, focusing on gut restoration after antibiotics may help reduce risks of immune-related conditions, such as food allergies and asthma—especially in children under age 2.
Antibiotics also increase the number of genes in the microbiome associated with simple sugar metabolism. That means minimizing added sugars after antibiotic use can help prevent a further imbalance in the gut.
Natural ways to restore gut health after antibiotics
Avoid unnecessary antibiotics
This should go without saying—but it’s still important to highlight. According to the American Academy of Pediatrics, 10 million antibiotic prescriptions are written unnecessarily for U.S. children every year. A common example: ear infections.
The AAP has updated their guidelines to reflect the “watchful waiting” approach based on certain criteria, since roughly 80% of ear infections clear on their own within 3 days without the use of antibiotics.
Reducing unnecessary antibiotic use not only protects your child’s long-term gut health, but also helps reduce the global threat of antimicrobial resistance.
Always talk with your healthcare provider about the best course of action for your child.
Feed the good bacteria
If your child has already started solids, diet is going to be critical in the weeks following antibiotic treatment while the microbiome is rebounding.
Focus on adding in fiber and as much diverse plant food as possible—that doesn’t necessarily mean veggies because I know this can be tricky!
Whole grains, spices and herbs, and fruits all count as plants too! So, go for a tri color quinoa blend, barley, and farro or lentil pasta noodles. Don’t shy away from using flavorful herbs and spices—they support the microbiome too.
Fermented foods like kefir, yogurt, coconut yogurt are all great options and tend to be pretty well accepted by most babies and toddlers.
If you are producing breast milk, consider increasing your child’s access to breast milk for the duration of the antibiotic course and at least a few weeks following, as breastmilk is uniquely designed to feed a growing child’s microbiome.
2. Minimize the bad bacteria
Just as important as what you do feed the gut is what you don’t.
Try to minimize added sugars (even natural ones), as these preferentially feed the less-beneficial microbes.
Same goes for refined flours, which lack complex fiber and can promote imbalances in the microbiome.
I know it can be challenging, but think of this as a short critical window—I recommend aiming for a month— with maximum benefits for your child’s long-term health and resilience.
3. Stay Hydrated
While your child is rebuilding from antibiotics, it’s important to keep them hydrated to aid digestion and prevent constipation.
If they are not drinking much water, consider a bit of fruit blended with water and frozen into an ice pop.
4. Play outside
Time out in nature goes a long way towards contributing to a child’s microbiome, and children nowadays are spending less time outside than previous generations.
Especially now, let your child explore the dirt, splash in puddles, and cuddle with pets. These experiences introduce beneficial microbes in a natural way that strengthens the gut.
photo credit: Tatiana Syrikova
5. Lots of rest
Sleep is one of the most powerful (and often overlooked) tools for helping heal your child’s gut after antibiotics.
During deep sleep, the body goes into repair mode—restoring cells, calming inflammation, and helping beneficial gut microbes rebalance and grow.
Lack of sleep, on the other hand, can increase stress hormones and disrupt digestion, making it harder for the gut to bounce back.
So consider holding off on any events that may cut into your child’s sleep to give their body the time and space it needs to truly heal from the inside out.
What to eat to restore good gut bacteria after antibiotics
The good news is that the microbiome is quite resilient when fed the proper things.
Specific foods to focus on during this period are ones that contain prebiotic fiber, polyphenols and beneficial bacteria such as:
Fermented foods like yogurt, kefir, sauerkraut, fermented pickles and kimchi
Leafy greens (even if it's just blended into a smoothie)
Berries
Pears
Garlic
Oats
Broccoli
Asparagus
Less-ripe bananas
Chia seeds
Beans & lentils (check out my gut-healthy bean muffin recipe here!)
Herbs & spices (cilantro, dill, cinnamon, ginger, cumin etc.)
photo credit: ShotPot
A note on yogurt
Yogurt can be an excellent food to help restore the gut microbiome during this time, but it is best to opt for plain, full-fat yogurt since flavored versions usually are loaded with simple sugars.
If your child is not interested in unsweetened yogurt, try adding it to smoothies with fruit, or mix with herb packets for a flavorful ranch dip.
Should I give my child probiotics? If so—should I start before or after the antibiotics are finished?
Yes, probiotics can help—but timing and type matter.
The best approach is to start probiotics during the antibiotic course and continue for several weeks afterward. This can reduce side effects like diarrhea, tummy aches, and even yeast infections (thrush).
I often recommend Culturelle with L. rhamnosus GG, one of the most well-researched probiotic strains for kids taking antibiotics. They make infant drops as well as powders for toddlers and older children.
You might also consider Saccharomyces boulardii, a probiotic yeast that isn’t affected by antibiotics and has been shown to benefit children taking antibiotics.
While probiotics have a long safety record, it's always advised to consult with your child’s pediatrician or healthcare professional on your child’s specific needs before introducing any probiotic supplement, especially to infants.
To get the most benefit, it's recommended to take your probiotics 2-6 hours apart from the antibiotic dose, to give them the ability to provide a benefit in the body, as probiotics strains are still susceptible to most antibiotics themselves. Even still, specific probiotics have been shown to provide benefits taken alongside antibiotics.
As I mentioned before, you’ll want to provide plenty of fermented foods, but foods like yogurt and kefir which contain a lot of calcium should be consumed 2 hours away from antibiotics, as they can make certain antibiotics less effective.
If we need to give our kids antibiotics, we want them to be as effective as possible to get rid of the threat and have less chance of creating antimicrobial resistance.
Another benefit of taking probiotics alongside antibiotics is that strains like L. rhamnosus GG to help to reduce the risk of antimicrobial resistant organisms.
How long does it take to restore good gut bacteria after antibiotics?
Research shows that most gut bacteria in the microbiome can rebound to similar pre-treatment levels within a couple months of stopping the antibiotic. Although, certain bacteria can remain undetected for months or even years after treatment.
A 2025 study on children (mostly taking amoxicillin) found that while many aspects of the microbiome recovered within a month, it took up to 12 months for Bifidobacterium levels to return to normal.
That’s why continuing to feed the gut well over the long term—through fiber-rich foods, outdoor play, and rest—is one of the best things you can do to mitigate the downsides of antibiotics for our children.
Bringing it all together
Supporting your child’s gut health after antibiotics doesn’t have to feel overwhelming.
With just a few intentional steps—like nourishing them with the right foods, encouraging outdoor play, prioritizing rest, and considering targeted probiotics—you can help their microbiome bounce back and set the stage for lifelong wellness.
Remember, the gut is incredibly resilient, and every small choice you make adds up.
If you found this guide helpful, I’d love for you to share it with another parent who might need it—and be sure to grab my free gut-friendly meal guide for kids to make your post-antibiotic prep even easier!
