The Best Probiotics and Diet Strategies to Restore Your Gut After Antibiotics

If you’ve just finished a course of antibiotics and now feel bloated, foggy, or “off,” you’re not imagining it. While antibiotics can be essential and even life-saving, they often leave your gut in a depleted state — wiping out the good bacteria along with the bad.

The good news? Your gut can recover. With the best probiotics and supportive dietary strategies, you can restore your microbiome naturally and feel like yourself again after taking antibiotics.

In this post, we’ll walk you through the most effective, evidence-based probiotics to take after antibiotics — plus the foods that can help your gut bounce back stronger than ever after antibiotics.

Why Antibiotics Disrupt Gut Health

Antibiotics work by killing off harmful bacteria that cause infection — but they don’t discriminate. They also wipe out the beneficial bacteria that support digestion, hormone balance, and immune function.

Even a single course of antibiotics can:

Reduce microbiome diversity

Damage the gut lining

Increase risk of antibiotic-associated diarrhoea

Trigger bloating, food sensitivities, or fatigue

 

Restoring your gut microbiome after antibiotics is essential, not optional — especially if you're in midlife and already dealing with digestive or hormonal shifts. Studies show it can take months, if not years to restore your gut after antibiotics if you don't take the steps needed to heal your gut after antibiotics.

Should you take Probiotics during your Antibiotic treatment?

This is not a straightforward yes or no answer. I tell my patients that if it is a short course of antibiotics (10-14 days), they should wait until after their treatment has finished. The antibiotics will kill off a lot of the probiotics that you are taking, meaning you wont get much bang for your buck out of the probiotics that you are taking.

What you should do is take a probiotic yeast called Saccharomyces boulardii (SB). Because SB is a yeast and not a bacterium, the antibiotics will not kill the SB. Instead SB will protect your gut lining and your microbiome, reducing the total damage done by the antibiotics. SB will also reduce symptoms associated with antibiotic use, such as diarrhoea.

Once you have finished your antibiotics, then you can start your probiotics (see details below), along with the SB for six weeks.

If you are on long-term antibiotics, such as acne, then you need to take probiotics alongside your medication. Taking your probiotics at least 2 hours away from your antibiotics will reduce the medication killing your probiotics. With long-term medications, doing your best to maintain gut health is essential. You should also take SB with your probiotics.

Best Probiotics to Take After Antibiotics

Not all probiotics are created equal. The strains below are backed by clinical research for their effectiveness in restoring gut balance after antibiotic use.

1. Lactobacillus rhamnosus GG (LGG)

One of the most researched strains, LGG helps:

Prevent antibiotic-associated diarrhoea (AAD)

Support gut lining repair

Reduce post-antibiotic bloating

 

Suggested dose: 10–20 billion CFU/day

2. Saccharomyces boulardii

This beneficial yeast survives antibiotics and protects the gut from imbalances like Clostridium difficile overgrowth. It also supports immune modulation and gut barrier function. This is the strain that you should be taking DURING antibiotic use. It has a protective effect on the gut wall and will reduce symptoms associated with antibiotics use such as diarrhoea and stomach pains.

Suggested dose: 5–10 billion CFU/day

3. Lactobacillus acidophilus (e.g., NCFM strain)

Restores healthy bacteria in the small intestine and helps reduce bloating, gas, and discomfort post-antibiotics.

Suggested dose: 1–10 billion CFU/day

4. Bifidobacterium lactis (e.g., HN019 strain)

Supports colon health and bowel regularity while enhancing the production of short-chain fatty acids for gut lining repair.

Suggested dose: 5–20 billion CFU/day

5. Lactobacillus plantarum (e.g., 299v strain)

A powerful anti-inflammatory strain that protects the gut lining and reduces digestive symptoms like cramping or sensitivity.

Suggested dose: 10–20 billion CFU/day

 

Gut-Healing Foods to Eat After Antibiotics

While the best probiotics are key, food plays a powerful role in rebuilding your gut microbiome after antibiotics. Here’s how to use diet as your daily gut therapy:

1. Focus on Fibre-Rich, Plant-Based Foods

Your beneficial gut bacteria feed on fibre — particularly prebiotic fibres that help them repopulate and thrive.

Aim for 30+ different plant foods each week, including:

Vegetables: leafy greens, sweet potato, broccoli, beetroot

Fruits: berries, apples, pears, bananas

Legumes: lentils, chickpeas, black beans

Whole grains: oats, quinoa, buckwheat

Nuts & seeds: chia, flax, almonds, pumpkin seeds

 

Diversity = microbial diversity = faster recovery.

2. Add Fermented Foods for Natural Probiotics

Fermented foods are natural sources of live beneficial bacteria that support microbiome repair.

Include small daily amounts of:

Natural yoghurt (unsweetened)

Kefir

Sauerkraut, kimchi

Miso, tempeh

Start slow if your gut feels sensitive.

3. Include Prebiotic Foods

Prebiotics are like fertiliser for your probiotics — they help the good bugs grow.

Top prebiotic foods:

Garlic, onions, leeks

Asparagus, Jerusalem artichokes

Green bananas

Cooked and cooled potatoes or rice (resistant starch)

Tip: Pair prebiotics with your probiotics for a synergistic effect.

4. Try Bone Broth or Collagen-Rich Foods

These help repair the gut lining and soothe inflammation, especially if antibiotics caused irritation

Enjoy:

Slow-cooked bone broth

Chicken soup

Gelatin-based recipes

These are rich in glutamine and glycine, amino acids that support gut integrity.

Foods to Avoid During Gut Recovery

Certain foods can slow your progress or trigger symptoms during recovery. Avoid or limit:

Ultra-processed foods

Artificial sweeteners (especially sucralose and aspartame)

Excess alcohol

Added sugar

NSAIDs like ibuprofen (unless medically necessary)

These can worsen inflammation and delay microbiome rebalance.

How Long Should You Take Probiotics After Antibiotics?

For most people, continuing probiotics for six weeks post-antibiotics is ideal. Some women with recurring symptoms (like bloating or IBS) may benefit from a longer course or targeted gut repair protocol.

Ready to Rebuild Your Gut with Confidence?

If your digestion still feels unsettled after antibiotics — or you’re just not feeling like you — I can help.

My Gut Reset Program is designed for women in midlife who want to restore gut balance naturally, reduce bloating, and get their energy back without guesswork.

Final Thoughts on Finding the Best Probiotics

Restoring your gut after antibiotics isn’t just about adding a probiotic capsule. It’s about feeding your microbiome, healing your gut lining, and reducing inflammatory triggers.

By combining the best probiotics with a fibre-rich, anti-inflammatory diet, your gut can bounce back naturally — and take your energy, mood, and digestion with it.