Gut Problems After Antibiotics: What’s Happening?

Antibiotics are often necessary to treat infections, but many people notice digestive problems after finishing a course.

If your gut hasn’t felt the same since taking antibiotics, this is very common — and it’s not something you have to just “wait out”.

How antibiotics affect your gut

Antibiotics work by killing bacteria that cause infection.

The issue is that they also reduce the good bacteria in your gut — the ones that help with digestion, bowel regularity, and overall gut health.

When these helpful bacteria are reduced, your gut can become out of balance. This can lead to digestive symptoms that continue even after the antibiotics have stopped.

Why do I feel worse after finishing antibiotics?

Antibiotics don’t just kill the “bad” bacteria—they also reduce beneficial gut bacteria.

When treatment ends, your gut microbiome is temporarily out of balance, which can cause symptoms even though the infection is gone.

What exactly happens to my gut after antibiotics?

After antibiotics:

  • Good bacteria are reduced
  • Harmful or opportunistic microbes may temporarily overgrow
  • Digestion and fermentation change
  • The gut lining can become more sensitive

Is it normal to have diarrhoea after antibiotics?

Yes. Very common.

  • Antibiotics alter how your colon absorbs water
  • Bacteria that normally control stool consistency may be reduced

Why am I bloated or produce wind after antibiotics?

Without enough beneficial bacteria:

  • Food ferments differently
  • Gas-producing microbes may dominate temporarily
  • Digestion of fibre, sugar, and lactose may be impaired

Can antibiotics cause constipation instead of diarrhoea?

Yes. Some people experience:

  • Slower gut motility
  • Reduced microbial signals that stimulate bowel movement
  • Changes in bile metabolism

Can antibiotics cause acid reflux or stomach pain?

Yes. Antibiotics can:

  • Irritate the stomach lining
  • Alter acid regulation
  • Affect gut-brain signalling

Symptoms often include nausea, burning, or upper abdominal discomfort.

Why do I feel fatigued or “off” after antibiotics?

Gut bacteria help produce:

  • Certain B vitamins
  • Short-chain fatty acids (energy for gut cells)
  • Neuroactive compounds

When these drop, people may feel tired, foggy, or low.

Can antibiotics affect mood or anxiety?

Yes. The gut–brain axis means microbiome changes can influence:

  • Anxiety
  • Low mood
  • Irritability
  • Brain fog

This is usually temporary, but very real.

Can antibiotics cause yeast overgrowth or thrush?

Yes. When bacteria are reduced, yeast (like Candida) may overgrow, leading to:

  • Oral thrush
  • Vaginal yeast infections
  • Increased sugar cravings

Should I take probiotics during or after antibiotics?

So yes, as you can see from the questions above antibiotics can be tough on your gut. Probiotics help protect and rebuild your good bacteria during and after treatment. Adding a probiotic can make recovery smoother and support overall gut health.

Taking probiotics during antibiotics:

  • Probiotics may help replace some of the good bacteria that antibiotics kill.
  • They can lower the chance of antibiotic-related diarrhoea.
  • Take the probiotic at least 2 hours apart from the antibiotic so the antibiotic doesn’t kill the probiotic.

Taking probiotics after antibiotics:

  • Probiotics can help restore healthy gut bacteria once the antibiotic course is finished.
  • This may help your digestion return to normal more quickly.

Best approach:

  • It is recommended taking probiotics during the antibiotic course and continuing for 3 to 4 months after finishing antibiotics.

Not Sure What’s Right for You?

  • Everyone’s gut is different. The best probiotic type, dose, and timing can vary based on your health, medications, and symptoms.
  • Ask us for help to choose the right probiotic plan and protect your gut health during and after antibiotics.