The Toilet Chronicles: How Long COVID messes with your gut — and what you can do about it.
Why Has My Poo Changed After COVID?
COVID can affect your digestive system, and some people experience changes in bowel habits for weeks or months after infection. These may include diarrhoea, constipation, bloating, unusual stool consistency or alternating between the two.
Possible explanations include changes in gut movement, the microbiome, post-infectious irritable bowel syndrome (IBS) and autonomic dysfunction. However, not every bowel change after COVID is caused by Long COVID. Medication, diet and unrelated digestive conditions can produce similar symptoms.
Persistent changes, particularly with bleeding, unexplained weight loss or significant pain, should be assessed by a healthcare professional.
Key Stats & Insights
- 10.8%: A 2023 systematic review estimated the prevalence of persistent gastrointestinal symptoms after COVID at 10.8%, although results varied substantially between studies.
- 154,068 people: A large study published in Nature Communications found increased risks of several gastrointestinal conditions in the year following COVID, including diarrhoea, constipation and IBS.
- Gut microbiome changes: Researchers have identified differences in gut bacteria in some people with Long COVID. Whether these changes directly cause symptoms remains under investigation.
These findings support a connection between COVID and digestive problems, but they cannot tell us why any particular person’s poo has changed.
The Toilet Chronicles: When Your Gut Joins the Party
I never expected that after catching a virus best known for attacking the respiratory system, my colon would decide to join the party too.
Yet here we are.
In the world of Long COVID, even something as ordinary as going to the loo can become an event.
Diarrhoea. Constipation. Bloating. A digestive system behaving like a roller coaster nobody bought a ticket for.
If you’ve found yourself Googling “Why is my poo weird after COVID?”, you’re certainly not the only one asking.
And while talking about bowel movements isn’t everyone’s favourite conversation starter, these changes deserve attention.
What’s Going On in There? (The Gut, Not the Loo)
Your gut is a busy place.
It moves food along, absorbs nutrients and water, communicates with your nervous system and hosts trillions of microorganisms.
When everything works, you barely notice it.
When it doesn’t, you definitely do.
How might COVID interfere?
Researchers are investigating several possible explanations:
Changes in gut motility: The muscles and nerves controlling digestion may not move things along as they normally would. Faster movement can contribute to diarrhoea; slower movement can contribute to constipation.
Microbiome disruption: Studies have found changes in gut bacteria in some people after COVID. These changes may be relevant, but their exact role is still uncertain.
Post-infectious IBS: Some people develop IBS-like symptoms after an infection, including abdominal pain, bloating and altered bowel habits.
Autonomic dysfunction: The autonomic nervous system helps regulate digestion. Some people with Long COVID and POTS experience gastrointestinal symptoms alongside dizziness and palpitations.
There may be more than one explanation — and not every digestive symptom is necessarily caused by COVID.
For the deeper science, including microbiome research and inflammation, read our main Long COVID gut guide.
Diarrhoea vs Constipation: Two Sides of the Same Messy Coin
When It’s the Runs
Sometimes your gut seems determined to get everything out as quickly as possible.
You might experience:
- Loose or watery stools.
- Urgent trips to the toilet.
- Abdominal cramps.
- More frequent bowel movements.
Diarrhoea can occur after COVID, but other causes — including infections, medications and food intolerances — should also be considered.
What may help: Replace lost fluids, eat what you can comfortably tolerate and seek advice if symptoms persist.
If you have POTS, dehydration can make dizziness and other orthostatic symptoms worse. Follow your clinician’s advice about fluids and electrolytes rather than automatically increasing salt.
When It’s the Bung-Up
At the other extreme, your bowel decides:
Nope. Not today.
Constipation may mean hard stools, straining, fewer bowel movements than usual or feeling that you haven’t emptied properly.
Possible contributors include slower gut movement, reduced food or fluid intake, medication and changes in daily activity.
What may help: Gradually increasing fibre if appropriate, adequate fluids, a comfortable toilet position and discussing suitable treatments with a pharmacist or GP.
And if you’re severely affected by Long COVID, please ignore the assumption that everyone can simply go for a brisk walk.
Triggering post-exertional malaise to encourage a bowel movement isn’t a sensible trade-off.
Why Can Both Happen?
Some people alternate between constipation and diarrhoea.
This can happen with IBS, but it isn’t the only explanation.
Occasionally, watery stool can leak around a build-up of hard stool — known as overflow diarrhoea.
If you’ve been constipated and then develop watery leakage, particularly with bloating or discomfort, ask for medical advice rather than assuming you need an anti-diarrhoeal medicine.
Why Does My Poo Look Different?
Changes in stool aren’t always about how often you go.
Sometimes it’s the appearance that sends you straight to Google.
Hard, lumpy stools: Often associated with constipation.
Loose or watery stools: May indicate diarrhoea or faster intestinal transit.
Green stools: Can be related to diet, food colouring or faster movement through the bowel.
Yellow stools: May have several explanations, including diet and changes in digestion.
Mucus: Small amounts can be normal, but persistent or increased mucus with other symptoms deserves assessment.
Very pale stools: Particularly if accompanied by dark urine or yellowing of the skin or eyes, need prompt medical advice.
Black, tarry or bloody stools: May indicate gastrointestinal bleeding and require urgent assessment.
The occasional unusual poo doesn’t automatically mean something serious. But persistent or concerning changes shouldn’t simply be labelled Long COVID.
What Can You Actually Do?
Before buying probiotics, eliminating half your diet or starting a complicated gut-healing programme, try something simpler.
1. Notice what’s changed
Keep a brief record of:
- How often you’re going.
- Whether stools are hard, loose or watery.
- Any pain, bloating or urgency.
- New medications, supplements or foods.
You don’t need a 47-column spreadsheet. Three or four useful observations are enough.
2. Look after hydration and nutrition
Diarrhoea can cause fluid loss, while inadequate fluid intake can contribute to constipation.
Try to maintain a varied diet that you tolerate, without unnecessarily restricting foods.
If eating is difficult or you’re losing weight, ask for medical or dietetic support.
3. Be cautious with probiotics
The microbiome is an exciting research area, but there is no proven probiotic that fixes Long COVID gut symptoms.
Some products may help particular digestive conditions. Others may do nothing or worsen bloating.
More bacteria in a capsule doesn’t automatically mean better results.
4. Adapt advice to your energy limits
For people with PEM, severe fatigue or POTS, managing digestive symptoms must fit within what the body can tolerate.
That might mean keeping drinks nearby, choosing easier-to-prepare foods, getting help with meals or asking about medication rather than attempting an exhausting lifestyle overhaul.
The aim is to make life easier, not create another full-time job.
When Should You Speak to Your Doctor?
If bowel changes persist, keep returning or affect your ability to eat and function, speak to your GP.
Other conditions can cause similar symptoms, including coeliac disease, inflammatory bowel disease, thyroid problems and medication side effects.
Seek urgent medical assessment for black or dark-red stools or bloody diarrhoea. Heavy bleeding, collapse or severe symptoms may require emergency care.
Unexplained weight loss, persistent abdominal pain and significant changes in bowel habits also warrant investigation.
Having Long COVID doesn’t mean every new symptom should be automatically attributed to it.
The Big Takeaway
If your gut has been misbehaving since COVID, you’re not imagining the symptoms.
There is growing evidence that COVID can be associated with ongoing digestive problems, including diarrhoea, constipation and IBS-like symptoms.
But the science is still developing, and the cause won’t be the same for everyone.
You can make small adjustments, track changes and seek appropriate medical advice without turning your entire life into a gut-health experiment.
And perhaps one day, going to the loo will return to being the wonderfully boring activity it used to be.
Frequently Asked Questions
Can Long COVID cause diarrhoea?
Diarrhoea has been reported after COVID and may occur alongside other digestive symptoms. Persistent diarrhoea needs assessment because infections, medications and other conditions can cause it too.
Can Long COVID cause constipation?
Yes, constipation has been reported after COVID. Possible contributors include changes in gut motility, autonomic dysfunction, reduced intake and medication effects.
Why do I alternate between diarrhoea and constipation?
This pattern can occur with IBS, but other explanations are possible, including constipation with overflow diarrhoea. Persistent alternating symptoms should be discussed with a clinician.
Can COVID change my gut bacteria?
Studies have identified microbiome differences in some people after COVID. Researchers are still investigating whether these changes contribute directly to symptoms and which treatments might help.
Should I take probiotics for Long COVID gut problems?
There is no established probiotic treatment for Long COVID gut symptoms. Discuss persistent problems with a healthcare professional before spending money on multiple supplements.
Are bowel changes after COVID permanent?
Not necessarily. Symptoms may improve, fluctuate or persist, depending on their cause. New or ongoing changes should be assessed rather than assumed to be permanent.
Read Next: When Your Gut Has More Questions
Long COVID and the Gut: How Your Microbiome, Immune System and Brain Are Connected
Our main gut guide explores the bigger picture, including microbiome research, inflammation and the gut–brain connection.
Long COVID and the Gut: What the Microbiome Research Really Shows
A closer look at gut bacteria, dysbiosis and the evidence behind microbiome treatments. Particularly useful before investing in a cupboard full of supplements.
Why Did I Suddenly Develop New Food Intolerances After Covid?
For anyone whose previously harmless lunch now seems to come with an unexpected list of consequences.
Dysautonomia After COVID: A Personal Story of POTS, Symptoms and Recovery
Explore how autonomic dysfunction can affect different body systems, including digestion.
12 Essential Tips From Long Haulers on Managing Post-Exertional Malaise
Practical ideas for protecting your energy when ordinary daily activities are already exhausting.
How to Stop Long COVID Getting Worse
A broader guide to pacing, recognising triggers and avoiding unnecessary setbacks.
Medical Disclaimer
This article is for educational purposes and does not replace professional medical advice. Changes in bowel habits can have causes unrelated to COVID. Seek medical assessment for persistent symptoms, bleeding, unexplained weight loss, significant pain or other concerning changes.
Resources & References
- Xu E, Xie Y, Al-Aly Z. (2023). Long-term gastrointestinal outcomes of COVID-19. Nature Communications.
- A Systematic Review of the Prevalence of Persistent Gastrointestinal Symptoms and Incidence of New Gastrointestinal Illness after Acute SARS-CoV-2 Infection. (2023).
- NHS. Constipation.
- NHS. Bleeding from the bottom (rectal bleeding).
- NHS. Symptoms of bowel cancer.