Is Coffee Bad For Gut Health?

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It’s no secret that coffee and the bathroom are often related. If you’ve noticed that, you wouldn’t be an isolated case. Many people have reported that within 30 minutes of a coffee – they have to poop! 

This can be alarming and lead us to question if coffee is harming our gut health, or is it actually helping us inside?

Not to worry – we’ve got that covered here. We’ll answer the big questions that keep you awake at night… or maybe that’s just the caffeine. 

Why Does Coffee Make You Poop? 

Most of us have experienced this one before! Coffee is full of caffeine. That fueling rush is about 95 mg of caffeine in a single cup, and that’s what gets us moving in the morning. From a zombie to perky in just a few sips, right? 

But it is the caffeine that could be the reason for your need to poop. Many studies have shown that caffeine can allow for quicker colon contractions. Basically – you know how coffee can help move you around quicker? Same applies to your gut! 

It’s important to note here that decaf coffee has also been known to get us going to the bathroom. Not to the same extent as our regular cup, but the numbers are still there.

And let’s not forget that our bowel is more active in the morning anyway – which is usually the best time for a coffee.

Coffee And Pooping – Is This A Good Thing For Our Gut Health? 

The pooping stimulated by the coffee leads to improved bowel movement that helps keep some constipation symptoms at bay. Constipation can lead to hemorrhoids, fecal impaction (hard painful poop that gets stuck in the rectum and can require manual removal – yikes!), and even incontinence of the bowel.  

What we have here in essence is a natural (and tasty) laxative. However, for some of us it can be exacerbated by other gut problems such as IBS (irritable bowel syndrome).

Those with IBS may already be experiencing discomfort and therefore, it would be better to avoid coffee altogether. 

Other changes to your gut with coffee could be related to added cream or sugar. About 30 million American citizens are, at least to some extent, lactose intolerant, and this becomes more common with age.

Lactose intolerance can lead to problems such as diarrhea, bloating or gas. If you’re lactose intolerant – avoid adding cream or milk to your beverage!  Lactose free dairy products like Lactaid (lactose free milk), almond milk or soy milk can be used instead.

Coffee And Your Gut’s Microbiome 

Your gut’s microbiome is an essential aspect of overall health. In fact, an unhealthy balance of good and bad microbes can contribute to weight gain, an increase in cholesterol or having higher blood sugar.

The good news for coffee drinkers though – the evidence suggests that coffee assists in the improvement of the microbiome and helps regulate your metabolism and aids your immune system. 

But, how is it doing this?

In short, coffee contains antimicrobial molecules that promote a more healthy gut – keeping bad bacteria at bay and supporting the good bacteria! 

Making Your Joe More Gut-Friendly 

If you’re someone who loves a coffee but often feels there’s a problem after it – there are ways to combat this. Why should you give something you love up altogether?

Unless something like IBS or Crohn’s disease is the culprit, you can simply change your coffee habits. Here’s some suggestions: 

  • Cool it down – Try creating cold-brewed coffee by mixing ground coffee with tepid or cold water. This method takes longer to produce the coffee (due to the water being cold) but it should also allow for a less acidic drink (in fact, around 65% less). Less acid = fewer gut problems.
  • Don’t panic though, you don’t need to drink it cold – warm it up in the microwave or pan and enjoy your cup of coffee!
  • Less acid: hone in on it – When you’re next at the store, check the labels on the coffee. Certain beans will be pre-labelled with “less acidic” or “low acid.” It is also a good idea to check where your coffee is coming from…
  • Check the geography – Did you know that coffee beans differ from place to place? Coffee beans are full of natural acids and continue to acidically change during their life-span.  Where coffee is grown can have a huge impact on their acidity and flavour. In areas such as Brazil or Venezuela, at a lower altitude, coffee will have a lower level of acidity. 
  • Check the history – Coffee can sometimes be altered by some to reduce acidity through processing the beans chemically. This is a real no-go area for people trying to avoid painful guts. 
  • Check the color – A dark roast typically will be lower in acid; so if you’re someone who is concerned about acid reflux for example – maybe it’s best to stick to the European coffees (Italy or France usually!) 

Why Are We Told to Reduce Our Coffee Intake By Some Experts? 

A fair question. If coffee has so many benefits for our gut health, then why do some experts suggest drinking less coffee? 

Generally speaking, it’s the caffeine that concerns some experts. 400 mg per day is seemingly the “go-to” number. Any more than that can start to be excessive.

However, it is important to speak with a healthcare professional before altering your diet in any way. 

Pros And Cons of Coffee: Should I Give It Up For My Gut Or Not? 

It’s now best to review and get to the crux of the debate. Let’s start with the good points; the pros for coffee!

Coffee Pros:

  • Some studies have suggested that coffee can improve certain gut-related health concerns such as gallstones, constipation and pancreatitis. However, it is debated in the scientific world. 
  • Caffeine can improve your mood which ultimately can affect your gut’s overall health. People with anxiety or depression often feel gut pains or have trouble with digestion. 
  • Coffee has been linked with the prevention of certain diseases. Researchers have suggested that a daily intake of coffee can reduce the risk of Alzheimer’s, colon cancer, Parkinson’s disease, heart failure, liver disease, type-2 diabetes and strokes. 
  • A study has shown that coffee can increase good bacteria in the gut. 

Coffee Cons: 

  • Everyone is different and due to subjectivity, it is impossible to provide a definitive answer. (If the experts can’t agree, then neither can we!) 
  • The gut benefits suggested in some of the studies may also apply to green tea along with various other teas – but it’s not exactly java is it? 


When it comes right down to it, your gut health is reliant on a healthy overall diet. Giving something up can come down to personal choice.

We certainly love a good cup of joe in the United States. In fact, 60% of us get our caffeine fix at least once a day. But is it good for our gut health?  

Yes, there is some evidence that coffee can benefit your gut and there are ways to enjoy coffee, even if you have gut problems such as lactose intolerance.

Coffee can be of great service for your energy levels and concentration, but it can’t cure illnesses such as irritable bowel syndrome. 

For other drinks associated with gut health, here are some useful articles:

Written and Medically Reviewed By

  • Chelsea Cleary, RDN

    Chelsea is a Registered Dietitian Nutritionist (RDN) specializing in holistic treatment for chronic digestive disorders such as Irritable Bowel Syndrome (IBS), SIBO, and Crohn’s disease. She educates patients on how they can heal themselves from their conditions by modifying lifestyle and dietary habits.

  • Julie Guider, M.D.

    Dr. Julie Guider earned her medical degree from Louisiana State University School of Medicine. She completed residency in internal medicine at the University of Virginia. She completed her general gastroenterology and advanced endoscopy fellowships at University of Texas-Houston. She is a member of several national GI societies including the AGA, ACG, and ASGE as well as state and local medical societies.