Does coffee kill probiotics

Does Coffee Kill Probiotics? (how caffeine destroys good gut bacteria)

Are you a coffee drinker but also wish to enjoy the benefits of probiotics in your gut? 

You’ve probably heard that coffee is bad for probiotics, can make your gut more acidic and less bacteria-friendly, and shouldn’t be consumed with your supplements. 

While studies on probiotics are limited, there’s some evidence that drinking coffee might actually help promote better gut microbiome diversity.

In short, the more you drink coffee, the more diversified strains can thrive in your gut.

Is there evidence for that claim? Does drinking coffee kill probiotics? How long after taking probiotics can you drink coffee? Is there a way to get the best of both worlds with a coffee that has probiotics?

Key Highlights:

  • The answer isn’t an absolute “yes” or “no”
  • Yes – coffee can kill your probiotics if you drink hot coffee together with taking probiotics
  • Yes – coffee can kill your probiotics if you drink it less than 30 minutes before taking probiotics
  • No – coffee isn’t likely to kill probiotics if it’s cold coffee 
  • No – coffee isn’t likely to kill probiotics if it’s taken at least 30 minutes after taking probiotics
  • If in doubt about the time interval or if you really prefer taking your probiotic and drinking coffee at the same time, you might want to consider a probiotic coffee product instead

Does Drinking Coffee Destroy Probiotics & Good Gut Bacteria?

I’m a heavy coffee drinker, so when I heard about the benefits of probiotics, I got curious: “Will coffee kill my probiotics?” I bet you’re as curious about the answer as I am.

Well, the answer isn’t an absolute “yes” or “no.”

In a 2019 study published in The American Journal of Gastroenterology, researchers studied the effects of drinking a lot of coffee vs. a low amount on the diversity and relative abundance of good bacteria in the study subjects’ gut.

They aimed to answer the question, “Does caffeine kill probiotics?

Surprisingly, the study discovered that higher coffee consumption can be associated with a broader diversity and higher relative abundance of good bacteria. 

Using DNA sequencing, they determined that heavy coffee drinkers have more anti-inflammatory bacteria, particularly Roseburia and Faecalibacterium species. These human study subjects also showed lower levels of potentially harmful bacteria such as Erysipela Clostridium species.

So, although we’ve heard a lot about coffee “killing” probiotics due to acidity and other reasons, it’s likely that the heat from the drink is the main thing that can harm the good bacteria in your probiotic supplement.

Can I Take A Probiotic With Hot Coffee?

Remember that you need good bacteria to be alive so they can reach your small intestines where they can thrive.

Yes, the study above might have established that drinking more coffee doesn’t appear to interfere with probiotics. However, there’s no sense in killing these good bacteria with your hot coffee.

But does that mean you can’t drink hot coffee now? Well, it seems that the right timing when you take probiotics (before or after coffee) is the key to helping them survive.

How Long After Taking Probiotics Can I Drink Coffee?

As a rule of thumb, it’s ideal to take your probiotics on an empty stomach so that your stomach acids have not been activated yet. This gives them a chance to reach your small intestines as quickly as possible, without getting killed off by the harsh stomach acids.

Still, be sure to wait at least 30 minutes after taking your probiotics before you drink your coffee.

This way, there’s very little chance that the hot drink can come in contact with the probiotics. If possible, however, wait longer than 30 minutes (up to 10 hours is even recommended).

That’s because it is estimated that gastric emptying takes around 30 minutes after the meal. Then, it takes about 4 hours for small bowel transit, plus another 30 minutes to reach the colon.

The good news is that if you prefer cold coffee, then you wouldn’t have to wait that long.

Does Coffee Interfere With Probiotics If You Drink It First?

Now, suppose you want to drink coffee first. Will it have any effect on your probiotic if you space out taking them within 30 minutes or more?

Well, it’s actually a different story. It’s still best to take probiotics first, before drinking coffee.

The main reason is that coffee and other caffeine-rich foods or drinks are already acidic on their own. Although they’re not as acidic as your harsh stomach environment, they can increase the acidity of your gastric secretions.

In short, drinking coffee can make your already acidic stomach even more acidic. The higher your stomach acidity, the harsher environment it would be for your probiotics to survive.

And while coffee’s acidity isn’t likely enough to kill all your probiotics, the harsher stomach environment can. 

So, always take note of this rule: only drink coffee after probiotics – and make sure you wait at least 30 minutes.

Does Coffee Kill Probiotics In Yogurt?

Yogurt is known to be rich in probiotics. The same rules above apply:

  • Don’t mix hot coffee with yogurt because the high temperature can kill the probiotics
  • It’s better to eat the yogurt and wait at least 30 minutes before drinking coffee
  • Don’t eat yogurt within an hour or so after drinking coffee because the caffeinated drink can make your stomach more acidic, increasing the chances of your probiotic bacteria dying from the harsher environment

Special Coffee Products with Probiotics

Here’s good news if you’re still afraid that your coffee might kill the good bacteria in the food supplements you’re taking: there’s actually probiotic coffee!

Scientists who love coffee have found a way to let us drink our favorite brew without worrying about killing the probiotics. Let me explain it to you below.

What’s Probiotic Coffee?

A probiotic coffee is similar to your regular coffee but has a type of probiotic bacteria (usually varied strains of Bacillus coagulans). 

This coffee probiotic strain is made up of hardy bacteria that are different from the others because they aren’t heat sensitive – that means that they can survive being in a hot coffee drink and still have lots of viable strains that can colonize your gut.

In another 2019 study published in the Food Research International Journal, researchers discovered that Bacillus coagulans MTCC 5856 has a highly impressive survival rate even after brewing.

Based on this study, Bacillus coagulans MTCC 5856 had the following amazing survival rates despite the hostile environment during brewing:

  • 94.94% viability in unroasted green coffee 
  • 99.76% viability in tea

What’s more, adding water-soluble fibers (prebiotics) during brewing increased the probiotics’ survival rate to a whopping 99% viability.

Of course, this only applies to special probiotic strains such as Bacillus coagulans species.

So, if you’re planning on taking a probiotic coffee, it’s best to consider one that contains 1) these hardy probiotic species and 2) prebiotics or water-soluble fibers.

The 3 Best Probiotic Coffees

Here’s a short probiotic coffee review of my three favorite choices:

1. Gut Power Coffee – Prebiotic & Probiotic Gut Health Drink

CFU: 1 billion

Dosage: 1 serving (1 scoop) per day

Probiotics Strains/Strains: Bacillus coagulans GBI-30 6086

Form/Type: Powdered coffee drink

Certifications: Not indicated

Storage: Shelf-stable; refrigeration not required, but must be stored in a cool, dry place

Cost: $44 per pack (20 servings per pack) of 6.7 oz or 190 g

I love that this probiotic contains Bacillus coagulans GBI-30 6086 because this probiotic strain has been shown in studies to survive high heat during brewing.

Based on the study mentioned above, prebiotic fibers increase the viability of Bacillus coagulans to 99% – that’s why this product is ideal because it contains 6 g of Sunfiber PHGG (partially hydrolyzed guar gum), a type of prebiotic.

It’s also made of real organic Colombian coffee. Because it isn’t synthetic coffee or just a coffee-flavored probiotic, it can taste delicious like regular coffee. You won’t even know it has probiotics inside.

Here’s more good news: Sunfiber is a low-FODMAP* prebiotic fiber that promotes digestion without digestive upset because it helps food move through your gut at just the right pace.

*FODMAP means “fermentable oligosaccharides, disaccharides, monosaccharides and polyols,” which are carbohydrates that your small intestines absorb poorly; they can cause digestive distress or stomach upset

In case you aren’t happy with the results from this probiotic coffee, the brand also offers a 60-day money-back guarantee.


  • Contains the clinically studied strain Bacillus coagulans GBI-30 6086
  • Contains low-FODMAP prebiotics
  • Has real food polyphenols
  • Free from common allergens such as dairy and gluten
  • Has no added sugars or artificial sweeteners
  • Has no fillers
  • Vegan-friendly


  • Can be more expensive than regular, capsule-based probiotics
  • Might cause stomach upset during the first few days of use, but this is likely to go away once your tummy is accustomed to the new microbiome; you can start with just half a scoop for the first few days to avoid gut issues
  • Not readily available in all stores or online outlets

Where to Buy

2. Bare Organics ENERGIZING Organic Coffee (Infused with Superfoods & Probiotics)

CFU: Not indicated

Dosage: 1 cup (11.3 g or 0.4 oz per cup)

Probiotics Strains/Strains: Bacillus coagulans

Form/Type: Single-serve cups

Certifications: USDA Organic certified (United States Department of Agriculture)

Storage: Shelf-stable; no need for refrigeration

Cost: $12.99 per box (10 single-serve cups per box) of 115 g or 4.05 oz

This delicious brew is made of organic Nicaragua arabica coffee packed in individual single-serve cups, so you never get the dosage or the taste wrong.

I absolutely love that this probiotic coffee contains different superfoods like:

  • Organic guarana (caffeine-containing plant)
  • Organic maca root powder (a type of Peruvian ginseng)
  • Organic cordyceps mushroom (a type of medicinal fungus)
  • Organic Schisandra (also known as the five-flavor berry)

Superfoods are foods with a very high nutritional density. They’re packed with more nutritional benefits than other foods, making them ideal for a healthier body. They can also boost your energy and improve your immune system.

Plus, the USDA Organic certification is a huge bonus because you’re assured of a product that comes from natural, non-GMO ingredients that have been cultivated without pesticides, antibiotics, or other potentially harmful chemicals.


  • USDA Organic certified
  • Gluten-free
  • Free from GMOs (genetically modified organisms)
  • Keto-friendly
  • Vegan-friendly


  • Can be more expensive than regular coffee drinks or probiotic supplements

Where to Buy

3. Four Sigmatic Mushroom Ground Coffee with Probiotics

CFU: 1 billion

Dosage: 4 tbsp (21 g or 0.74 oz)

Probiotics Strains/Strains: Bacillus subtilis

Form/Type: Ground coffee 

Certifications: USDA Organic certified and Fair-trade certified

Storage: Shelf-stable; doesn’t require refrigeration but needs to be stored in a cool, dry place

Cost: $20 per pack (16 servings per pack) of 340 g or 12 oz; discounted price of $16 per pack with a subscription

This ground coffee is made of gut-supporting ingredients that can also boost your immune system:

  • Organic Chaga mushroom
  • Organic turkey tail mushroom
  • Organic yacon juice powder

I love that this brand also contains prebiotics, which can boost your probiotics’ viability, based on the study mentioned above.

The ingredients can also promote smooth digestion, boost your energy, and encourage a long-term positive mood.

Easy on your tummy, this brand contains the heat-resistant probiotic strain Bacillus subtilis, which is different from what the two other brands above use.

It’s also made of Fair Trade-certified, single-origin Arabica coffee beans that are sustainably and organically grown in Quetzaltenango, Guatemala, for a delicious probiotic drink.


  • USDA Organic certified
  • Gluten-free
  • Paleo-friendly
  • Vegan-friendly


  • Can be more expensive than regular probiotic supplements or coffee drinks 

Where to Buy

  • Four Sigmatic official website:  $20 per pack of 340 g or 12 oz (good for 16 servings per pack); you can get this for a discounted price of $16 per pack with a subscription

Conclusion & Suggestions

Some studies show that the more you drink coffee, the more diversified strains can live and thrive in your gut.

Just make sure that you take your probiotics first, and wait at least 30 minutes before drinking coffee to give your good bacteria a head start through your gut. This can increase their chances of reaching your gut.

Similar Posts

Leave a Reply

Your email address will not be published. Required fields are marked *