Does Coffee Kill Gut Bacteria? (All Facts Spilled)

Scientists love to study coffee, and we can’t blame them as about 2.25 billion cups are consumed around the globe daily—the most debated drink when it comes to health. 

Coffee is a double shot. It has many health benefits as well as side effects. The average amount recommended by a health professional is okay. The problem starts when you get addicted to it and start consuming 4-5 cups a day.

Coffee reduces the risk of diabetes or various types of cancer. But have you ever wondered how coffee affects gut bacteria – the good guys, microorganisms living in our digestive tract, and affecting our overall health?

Does coffee kill bacteria? No, coffee does the opposite. Instead, studies have shown that coffee drinkers have healthier gut bacteria than non-drinkers. 

Short Answer: Coffee does not kill gut bacteria. Caffeine in coffee stimulates stomach acid and activates contractions in the digestive tract, which helps your gut to improve metabolism and protect the immune system. 

However, the exciting thing is that there are also studies that show that apart from caffeine, there are other compounds of coffee that can inhibit the production of stomach acid.

You don’t have to worry because most scientists are united about coffee is good for gut bacteria and overall gut health.

Read on to learn more about how coffee affects your gut system. Let’s dig in!

Is Coffee Bad for My Gut?

Coffee is good for your overall gut health. Gut bacteria are responsible for breaking down food, improving the immune system, and developing vitamins. Coffee triggers the release of gastric juices such as stomach acid. Stomach acid is an integral part of digesting food properly. 

Low amounts of stomach acid make the body prone to infection by reducing the ability of the stomach to absorb the vitamins and nutrients.

So, sipping away 2-3 cups of coffee a day can help produce enough amount of stomach acid that helpful gut bacteria to absorb food easily.

That’s the very reason we often feel the urge to go to the bathroom right after we finish one cup of coffee.

However, coffee can be harmful to people with gut issues like heartburn and IBS. Because drinking coffee with bad IBS irritable bowel syndrome or acid reflux can irritate your gut even more.

If you have irregular gastral, then coffee is likely to increase the regulation. Also, coffee contains acid that decimates the stomach lining, causing ulcers or gastritis in daily coffee drinkers.

So to conclude, if your gut is healthy and you don’t have any stomach issues, you can enjoy the coffee without any worry. 

Is Coffee Good for the Gut Biome?

Coffee is good for the gut biome – a collection of microorganisms including bacteria, fungi, viruses, archaea, and protists depends.

Coffee alone can not be responsible for 1000+ bacteria species that reside in our intestines. But coffee does help these friendly bacteria to function more effectively. 

Everyone’s gut biome is unique, so how coffee affects them differs also. Health professionals suggest that drinking coffee daily can lead to diverse bacterial microbiomes. This is good for your health because diversity is the critical component of a healthy gut.

Coffee helps you develop diverse and healthy gut biomes that further improve your overall health by training the immune system and regulating energy balance. 

However, a large intake of coffee can be harmful to your gut biome as it contains natural antibiotics properties. The large and unnecessary amount of antibiotics can disturb the gut biome. 

Other common triggers that imbalance your gut biome are:

  • Use of antibiotics
  • Use of steroids
  • Not being breast-fed as a baby
  • Exposure to toxins
  • Food allergies and sensitivities
  • Exposure to environmental molds
  • Being born by Caesarian section

For a healthy and happy gut biome, keep enjoying your coffee but make sure to incorporate a nutritious diet, probiotics, and regular exercise in your daily routine.

Can Coffee Destroy Gut Flora?

Substances in coffee can disturb the gut flora balance but not necessarily harm it.

What you eat the whole day disturbs your gut flora one way or another. However, the concept of “disturb” can be different in context, for healthy people vs. people with gut problems.

When you eat or drink something that imbalances the gut flora, it finds its way back to balance, and that’s how the human body works. We can’t label a beverage as terrible or good for health vaguely. It depends on how it is affecting the individual.

If you take your cup of coffee full of cream and sugar, then yes, the digestive tract of gut flora can be thrown a bit off, but then it recovers its balance because that’s what the body needs: Balance.

Watch the video below to know more about coffee’s impact on your gut health and immunity.

What Does Coffee Do to Your Gut Bacteria?

Coffee affects gut health in different ways. It can be an excellent go-to drink every day for people with a healthy gut. Let’s look into all the good and bad ways coffee is affecting your gut bacteria.

Coffee Keeps Things Moving

Once you finish your cup of coffee, you feel the urge to go to the bathroom. In other words, coffee can help you poop by stimulating the colon.

This is something we all have experienced firsthand, but this phenomenon of coffee making you poop is proven by studies.

This study here shows that coffee stimulates the level of the colon, similar to how a meal does. The study result shows that 23% stimulation of the colon by drinking regular coffee. For further elaboration, check out my other article on coffee and bowel movements.

Coffee Can Increase Bifidobacterium Species

The human body needs complex carbohydrates that ferment and feed the bacteria in the colon, which protect our digestive tract. Bifidobacterium is the bacteria that do this genus job. 

Bifidobacterium with several species feed on glucose and break it into SCFA short-chain fatty acids, which inhibit the gut wall and provide energy.

The International Journal of Food and Microbiology study results show that drinking regular coffee increases the good guy bifidobacterium. More good bacteria, better gut health!

Coffee also seems to increase another microbe Lactobacillus in our gut. 

The table below shows why these bacteria are good for our health, one more good point for coffee lovers. They can keep enjoying 2-3 cups of their favorite drink while knowing it improves their health and not the other way around.

Impact on HealthGut Microbe: Bifidobacterium Gut Microbe: Lactobacillus 
Energy Produced from 1 mol of glucose 2.5 ATP molecules2 mol of ATP and lactic acid
Susceptible to AntibioticsYesYes
Healthy Gut Bacteria

Coffee Helps Absorb More Antioxidants

According to many studies, coffee contains theobromine, an alkaloid that increases the absorption of polyphenols.

These antioxidants, along with curcumin and glutathione, are low in the human body biologically. Coffee does act as a source of polyphenols which is beneficial for our bodies to boost the absorption process.

On the flip side, coffee does have some side effects on your gut microbe.

  • Coffee plus a poor diet can cause acid reflux and GERD.
  • Coffee cause stomach acid and a high amount of stomach acid can cause the increased stimulation in the colon, which further causes diarrhea and dehydration. 

Coffee affects gut health in different ways. It can be an excellent go-to drink every day for people with a healthy gut.


There are no hard and fast rules to drink coffee, such as not following scientific proof of coffee’s effect on gut health.

If you have a healthy gut and take coffee in moderation, it can positively impact you. However, those who suffer from irritable bowel syndrome or Crohn’s disease should avoid coffee.

How coffee affects your overall health depends on multiple factors – genes, the quantity of coffee you daily consume, your immune system. A personalized approach to daily coffee intake will be the key to attain the best gut health.

Moreover, it is essential to know that it might be something other than coffee if you face gut problems. Coffee is not a problem, but how it is brewed and how much creamer you make it plus the quantity. All these factors can contribute to how the coffee will impact your gut health.

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Matt Marshall

As I learn more and more about coffee and coffee products I want to share all my learnings with you here on this website. I hope you find my articles useful and entertaining to read.

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