How to Heal Your Child’s Gut After Antibiotics | A Simple Protocol
Wondering how to support your child’s gut health after antibiotics? Discover a simple, natural protocol with probiotics and targeted strains to restore balance, improve digestion, and strengthen immunity.
If your child has ever needed antibiotics, you know the mix of emotions that come with it. Relief, because antibiotics can be lifesaving. But also concern, because while they do their job, they can leave our kids with lingering tummy troubles, weaker digestion, or even immune struggles.
One of the most common questions I get is:
“How can I support my child during and after antibiotics?”
It’s such an important question, and one I’ve had to navigate in my own family.
Our Story
When my son was six, he had to take antibiotics for the second time in his life (the first was at birth). Not long after, his body was clearly struggling with chronic stomach aches, poor digestion, and just not feeling like himself.
I ended up running gut health labs on him. The same kind I now use with clients and the results were eye opening. His gut looked more like that of an unhealthy adult than a thriving child. That was my turning point. I knew we had to rebuild his gut from the ground up.
This is the exact protocol I wish I had known back then and what I now share with other parents who are walking this same road.
What Kids Need After Antibiotics
1. Probiotics During and After
Yes you can use probiotics while your child is still on antibiotics. Just separate them: antibiotics during the day, probiotics before bed.
Why bedtime? While we sleep, our bodies shift into “rest and digest” mode, giving probiotics a better chance to work.
Staying on a quality probiotic for at least 90 days post-antibiotics is key to restoring balance.
2. The Right Strains Matter
Not all probiotics are the same. Grabbing the first “kids probiotic” off the shelf usually isn’t enough. Different strains serve different purposes, and when antibiotics have wiped out so much, you need very specific ones.
The probiotic blend I trust most for kids post-antibiotics is Restore Flora from Microbiome Labs. It combines three clinically studied strains:
Saccharomyces boulardii – a probiotic yeast that’s been used for decades to calm gut issues after antibiotics.
Bacillus subtilis HU58 – helps crowd out harmful bacteria and supports digestion.
Bacillus clausii (SC-09) – works to recolonize the gut with beneficial bacteria.
Together, they support balance and help prevent unwanted strains from taking over.
3. Maintenance for Long-Term Gut Health
Once the gut is on the mend, it’s important to keep it supported. That’s where HU58 Bacillus subtilis really shines. It’s effective yet gentle, and research shows it helps with gas, bloating, diarrhea, and other digestive struggles that can linger after antibiotics.
This was a big piece of my son’s recovery and mine as well.
Our Antibiotic Recovery Protocol
Here’s the step by step plan we followed:
During + After Antibiotics
Month 1 – Restore Flora (open the capsule, mix into water or juice, and give before bed. Start with ¼ capsule for one week, then increase to ½ capsule for the rest of the month).
Months 2–3 – HU58 (same dosing: begin at ¼ capsule, then move to ½). Continue for at least 2 months, up to 3 if your child is still benefiting.
Months 4–6 (optional) – Transition to Kids MegaSpore Biotic Gummies. Begin with ½ gummy daily, then increase to 1 gummy if tolerated.
Note: These are for ages 3+ only.
If your child has already finished antibiotics:
Follow the same protocol, but no need to separate the timing from antibiotic doses.
How to Order Supplements
I make these practitioner grade supplements available to my clients and readers. You can create a free account through my link and use the CODE: kidsguthealing to receive 5% off all products.
It’s never easy to watch your child go through antibiotics, but you can support their little bodies as they recover. With the right probiotics and a thoughtful plan, their gut can bounce back strong and so can their overall health.
You’re not alone in this, and you don’t have to guess your way through it. There are tools to help, and they truly make a difference.
*Disclaimer: I’m not a doctor, and this isn’t medical advice. Always check with your trusted healthcare.
provider if you have questions about your child’s health. I’m simply sharing what worked for us, parent to parent.
💡 Follow @kellycarpenterwellness for more holistic nutrition and wellness tips.
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