Can you take a probiotic with coffee?

Written by: Kari Raman, PharmD, RPh
Published May 20, 2023

There is no strict rule on when you should take a probiotic in relation to coffee, but if you want to maximize the potential benefits of your probiotic, it might be best to take it 30 minutes before or 1-2 hours after drinking coffee. Coffee is acidic – and as explained in this medical article in The American Journal of Clinical Nutrition stomach acidity is a key factor that decreases the survival of probiotics in the stomach. This means coffee can potentially reduce the effectiveness of some probiotics, especially those that are sensitive to acidic environments.

However, it’s important to note that every individual is different, and the best time to take a probiotic may vary depending on the specific strain and your personal digestive system. Always follow the manufacturer’s instructions and consult with a healthcare professional if you have concerns or questions about your probiotic use.

When during the day is your stomach the least acidic?

The acidity level of your stomach fluctuates throughout the day, and it is generally the least acidic in the morning when you wake up. This is because your stomach produces less acid while you’re sleeping, as there is no food being consumed that requires digestion.

So if you like to have coffee when you wake up – and who doesn’t, right? – then consider taking your probiotic right away, brushing your teeth etc., making your coffee and then having that first sip about 30 minutes after you took the probiotic. 

Another alternative is to take your probiotic before bed, as your stomach is hopefully empty and your acid levels should drop during the night. This gives the probiotic some time to survive and multiply in your stomach while you are sleeping. 

How coffee impacts your stomach’s acidity – and therefore your probiotic’s survival

Coffee can have several effects on stomach acid levels, which, as we’ve already discussed, can impact how likely your probiotic supplement is to successfully colonize your gut. Some people who drink a lot of it may take antacids to reduce acidity; I’ve written an article on antacids and probiotics here. But let’s dive into acidity when you drink your morning brew:

Stimulates acid production: Coffee can stimulate the secretion of gastric acid in the stomach. Some researchers think that it’s the caffeine that does this, although I’ve seen studies that show that decaf also will spike acidic levels. It does this by increasing the production of certain hormones, like gastrin and cholecystokinin, which are responsible for stimulating the release of stomach acid. As a result, drinking coffee can lead to a temporary increase in stomach acidity.

Relaxes lower esophageal sphincter (LES): The LES is a muscular ring that separates the stomach from the esophagus. It helps keep stomach acid from flowing back into the esophagus, which can cause heartburn or acid reflux. Coffee, especially caffeinated coffee, can relax the LES, making it easier for stomach acid to flow back into the esophagus and cause discomfort, and possibly make it more challenging for the bacteria in your supplement to survive.

Increases bile production: Coffee can also stimulate the production and release of bile, which is an alkaline substance that aids in digestion. Medical researchers have found that bile can kill bacteria, and some kinds of non-coated probiotic supplements are particularly susceptible. So coffee, by causing bile production, can make it harder for your supplement to colonize the gut.

Can hot coffee kill probiotics?

Heat in coffee is unlikely to damage probiotics. You’ve got to get your drink really, really hot to kill bacteria – over 149 degrees fahrenheit. That temperature is probably going to cause third degree burns in your mouth and stomach – don’t ever drink any liquid that hot! 

The World Health Organization’s International Agency for Research on Cancer (IARC) has classified very hot beverages (above 65°C or 149°F) as “probably carcinogenic to humans” (Group 2A). This classification is based on limited evidence of an association between very hot beverages and an increased risk of esophageal cancer. You can check out one medical write up here. When you drink extremely hot liquids, they can cause thermal injury to the cells lining the esophagus, which may increase the risk of cancer over time.

In general, it’s a good idea to let your coffee cool down to a more moderate temperature before drinking it. Not only can this help prevent burns and reduce the potential risk of esophageal cancer, but it can also ensure that the heat does not negatively impact any probiotics or other supplements you may be taking. 

Can I dissolve probiotics in my coffee?

I wouldn’t suggest you dissolve your probiotic pills in your coffee, as it can be really hot until it’s cooled down enough for you to drink safely. Heat can damage or even kill some strains of probiotics, reducing their effectiveness and potential health benefits.

To ensure that your probiotics maintain their viability and efficacy, it’s best to wait until your coffee has cooled down to a safe drinking temperature (below 60°C or 140°F) before taking your probiotic supplement. Alternatively, consider taking the probiotic separately from your coffee, either 30 minutes before or 1-2 hours after drinking it. This will help ensure that the probiotic bacteria have the best chance of surviving and reaching your intestines, where they can provide their intended health benefits.

Is coffee bad for your gut microbiome? 

The effect of coffee on the gut microbiome is not completely understood and may vary from person to person, so I can’t really give any patient a straight answer on this question. Some studies suggest that coffee can have both positive and negative effects on gut health, depending on factors such as the individual’s existing gut microbiome, the type of coffee consumed, and the amount consumed.

Potential positive effects of coffee on the gut microbiome

Prebiotic effect: Coffee contains dietary fiber and polyphenols, which can act as prebiotics. Prebiotics are substances that promote the growth of beneficial bacteria in the gut. Dietary fiber is a type of carbohydrate that cannot be digested by the human body. It is fermented by bacteria in the gut, which produces short-chain fatty acids (SCFAs). By providing nutrients for the beneficial bacteria, coffee may help support a diverse and healthy gut microbiome.

Antioxidant properties: Coffee is a rich source of antioxidants, which can help protect cells in the body from damage caused by free radicals. Antioxidants in coffee may help reduce inflammation in the gut and promote overall gut health.

Potential negative effects of coffee on the gut microbiome

Increased acid production: Coffee can stimulate the production of stomach acid, which can lead to increased acidity in the stomach. This may negatively impact some bacteria in the gut, especially those sensitive to acidic environments.

Irritation and exacerbation of existing gastrointestinal issues: For some people, especially those with pre-existing gastrointestinal issues like irritable bowel syndrome (IBS), gastroesophageal reflux disease (GERD), or inflammatory bowel disease (IBD), coffee may exacerbate symptoms and cause irritation in the gut lining. This could potentially lead to an imbalance in the gut microbiome.

So don’t drink coffee in the hopes that it will be a magical prebiotic or something – drink it because you like it, because it helps wake you up, etc. And I strongly recommend moderation! 

Pharmacist Kari Raman

I’m Kari Raman PharmD, RPh, and I am a licensed, practicing pharmacist. I hold a Doctorate in Pharmacy from The University of the Pacific, and I’ve served patients in retail, compounding and hospital pharmacies.

Probiotics are confusing!

One of the most common questions I get asked by patients is about probiotics. And the truth is, probiotics are not as well understood by the healthcare community as they should be.

So I’ve been reading a lot of probiotic clinical trials, and sharing what I’m learning here.

I hope Pharmacist Probiotics helps you find out if there is a type of probiotic that works for you!