How To Repair Your Gut After Antibiotics

Antibiotics are powerful. Sometimes they’re essential; yet even when necessary, they often come with a cost. Because while antibiotics clear out harmful bacteria, they also sweep away the beneficial microbes that keep your digestion, immune system, mood, and energy in balance. They can be like using a flamethrower on a field.

You might notice the effects a few days or weeks later. Your digestion may feel off. Maybe you’re more bloated than usual, your skin flares, your sleep is disrupted, your energy dips, or you develop a yeast infection. For some, it’s a spike in anxiety or a general sense of feeling disconnected from their body. After all, your gut affects your mental health as well.

These are common signs that your microbiome is asking for support. Thankfully, you don’t need an extreme protocol or expensive supplement plan. What your body often needs most is steady, consistent care. The kind that feels doable and deeply nourishing.

Here’s how to begin rebuilding after antibiotics, in a way that supports both your gut and your overall wellbeing.

Feed The Good Bacteria That Remain

Your beneficial microbes haven’t disappeared. They’re just depleted and in need of support. Before jumping into high-dose probiotics, focus on feeding the good bacteria that are still there. Like tending to a garden after a frost, the goal is to nurture what remains and create a healthy environment for regrowth.

This is where prebiotic-rich foods make a big difference. These foods provide fiber that nourishes good bacteria and helps them grow stronger.

Try to include some of these:

Cooked and cooled potatoes, rice, or oats (which contain resistant starch)
Garlic, onions, and leeks
Green bananas or lightly cooked plantains
Asparagus, Jerusalem artichokes, and dandelion greens

Introduce these slowly if your digestion is sensitive. Even a few tablespoons a day can help gently encourage microbial diversity.

Reintroduce Probiotics Gradually

Probiotics can be useful, but they’re not a magic fix. If your system feels fragile, starting with small amounts through whole foods can be more tolerable than jumping straight into supplements.

Fermented foods offer a gentle, food-based way to reintroduce beneficial bacteria:

A spoonful of raw sauerkraut or kimchi
A small glass of kefir or ½ cup plain yogurt with live cultures
A few sips of pickle brine (from naturally fermented pickles found in the refrigerated section)

Start slowly. Pay attention to how you feel. It’s okay to pause or adjust if your body asks for something different.

Offer Your Gut A Period Of Rest

After a course of antibiotics, your digestive lining may be inflamed or more permeable than usual. This isn’t cause for panic, but it’s a good reason to simplify. Instead of jumping into a restrictive cleanse or elimination diet, focus on meals that are gentle, warm, and easy to digest.

For a week or two, aim for:

Home-cooked meals made from whole ingredients
Soups, stews, and well-cooked vegetables
Bone broth or vegetable stock to support repair
Lightly cooked oats or chia pudding for soothing fiber

Reduce sugar, alcohol, and any ultra-processed foods during this time. These can feed the wrong kinds of microbes and hinder the healing process.

By removing a few irritants and offering calm nourishment, you allow your gut to do what it’s designed to do – repair.

Support The Whole Ecosystem

Your microbiome doesn’t operate in isolation. It responds to your rhythms, your stress, your sleep, and your movement. To fully support gut repair, you’ll want to create a supportive environment beyond food alone.

Start here:

Hydration: Sip water throughout the day. Dehydration can slow digestion and make everything feel more sluggish.
Sleep: Deep rest helps your gut reset. Your circadian rhythm and microbiome are closely linked, so consistent sleep is part of the repair process.
Movement: Gentle walking, stretching, or restorative yoga can help stimulate digestion and reduce bloating.
Nervous system care: Chronic stress can disrupt your microbiome. Carve out small moments for stillness, even if it’s just two minutes of deep breathing before meals.

None of these steps needs to be rigid. Think of them as invitations, not rules. You are invited to actively cultivate your microbiome. Over time, they create the conditions your body needs to regain balance.

Everyone’s recovery timeline is different. For some, things begin to settle within a week or two. For others, it may take longer to feel steady again, especially after repeated antibiotic use or if your gut was already under stress beforehand.

What matters most is listening to your body and responding with care. You don’t need to rush or get it perfect. Just take one step at a time and let the process unfold.

The body knows how to heal. Your job is simply to support that process with patience, attention, and the building blocks it needs for the task.

P.S. If you have advanced notice about taking antibiotics, such as related to an upcoming surgery, I have good news. There is a type of probiotic you can take that can provide some protection for your microbiome.

It is a spore-based probiotic that isn’t damaged by antibiotics. You can easily order it here, right from my dispensary!