You Have To Take Antibiotics, Now What? Skip to content
 

You Have To Take Antibiotics, Now What?

You Have To Take Antibiotics, Now What?

I’ve been on antibiotics for two weeks to treat endometritis, and I’ll be honest, I’M FEELING IT MR.KRABS. The low-grade nausea, the heaviness in my stomach, the tummy gurgles…

But although medication is demonized in the wellness space, I know the benefits will outweigh the cons and I will get through it, but not without a strategy. 

Antibiotics can absolutely impact the gut microbiome, but that doesn’t mean you’re helpless. There are a lot of ways to protect your gut during treatment and intentionally rebuild it afterward.

Here’s exactly what I’m doing (and what research generally supports) if you want to navigate antibiotics in a way that still respects your long-term gut health. Remember, this is not medical advice and always check with your doctor! 

How to Support Your Gut During Antibiotics

Antibiotics reduce bacterial diversity, which is why probiotics can be helpful during treatment. Take probiotics 2–3 hours away from your antibiotic dose so they aren’t immediately wiped out. In my case, I’m taking Lady Bugs by Ora, which is designed to support the vaginal microbiome. That’s particularly helpful when treating infections like endometritis because the vaginal and uterine microbiomes are closely connected. 

Eat fiber that feeds beneficial bacteria

Even while taking antibiotics, your gut bacteria still rely on fiber as fuel.

Focus on easy-to-digest sources like:

  • Cooked vegetables

  • Berries

  • Avocado

  • Chia seeds

  • Ground flaxseed

If your stomach is sensitive (which can definitely happen on antibiotics), cooked foods are often easier than raw salads. I also personally like to supplement prebiotic fiber, it can also help with nausea and overall gut health! 

Support the gut lining

Antibiotics can sometimes irritate the intestinal lining, which is why nutrients that support gut integrity can be helpful.

Some supportive nutrients include:

Include small amounts of fermented foods

Fermented foods can introduce beneficial microbes that help maintain microbial balance.

  • Sauerkraut

  • Kimchi

  • Coconut yogurt (coconut cult!!)

  • Kefir (if you tolerate dairy)

Reduce things that make gut disruption worse

Certain things can worsen antibiotic-related dysbiosis or digestive symptoms.

It can help to limit:

  • Alcohol

  • Ultra-processed foods

  • Excess sugar

  • Artificial sweeteners

These are things I don’t normally have anyway but always like to add it in as a reminder, these things are just really never good for you hehe

Support digestion and nausea

Antibiotics can slow digestion and create that low-grade nausea feeling many people experience (like me rn)

Some gentle supports include:

  • Ginger tea or Peppermint tea

  • Lemon water before meals

  • Digestive bitters

  • Eating smaller meals instead of large ones

Stay well hydrated

Antibiotics increase your body’s metabolic workload and can increase fluid needs.

Hydration helps your body process medications and maintain electrolyte balance. My favorite clean hydration is here, I always go for Minerals & Chill! 

How to Rebuild Your Gut After Antibiotics

Once antibiotics are finished, the focus shifts from protection to rebuilding your gut health in a beneficial way. The microbiome is resilient, but it does take time.

Do not stop your probiotics after antibiotics!!! I found this really cool brand called Good Bacteria (working on a code for you guys soon) and they have a 4 week protocol of tailored probiotics that shift from week to week to re-populate your gut bacteria in a meaningful way. It’s pretty tasteless but you can add it to juice or something but it’s something I am going to recommend to everyone that’s looking to rebuild their gut in a simple way. 

Increase prebiotic foods

Prebiotics are compounds that feed beneficial gut bacteria.

Some of the best foods include:

  • Garlic

  • Onions

  • Leeks

  • Asparagus

  • Green bananas

  • Cooked and cooled potatoes or rice

These help beneficial bacteria regrow.

Increase plant diversity

Research suggests that eating 30 or more different plant foods per week is associated with greater microbiome diversity.

Consider gut-supportive supplements

  • Certain supplements may help support microbiome recovery and gut lining integrity. These are helpful even if you aren't on antibiotics but want to just have a health gut. 

Examples include:

  • Sodium butyrate – supports colon cell health, an absolute must for overall digestion (code: ILLIE20)

  • L-glutamine – helps nourish intestinal cells

  • Collagen or bone broth – provides gut-supportive amino acids
  • Saccharomyces boulardii – a beneficial yeast often used alongside antibiotics (you can find this typically in the fridge section at Whole Foods)

Eat polyphenol-rich foods

Polyphenols act as fuel for beneficial microbes and help support microbial diversity.

  • Pomegranate

  • Berries

  • Extra virgin olive oil

  • Green tea

  • Dark chocolate (dont gotta tell me twice)

Support liver detox pathways

When bacteria die off and antibiotics are metabolized, the body produces metabolic waste that must be processed by the liver.

Helpful foods include:

  • Cruciferous vegetables (broccoli, cauliflower, cabbage)

  • Sulfur-rich foods (garlic, onions, eggs)

  • Adequate protein

  • Liver Tincture from Zuma, Symbi or a Tea Version

Taking antibiotics when they’re needed doesn’t make you less “holistic” it just means you’re taking care of an infection that could otherwise cause much bigger problems like in my case endometritis which could be preventing conception. The real empowerment comes from knowing that your health isn’t fragile. Your body is resilient. Your microbiome can recover and when you support it intentionally, it often does.

 

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by Iliriana Zeneli – March 11, 2026