Is Coffee Bad For Gut Health?

Coffee tends to have that ‘guilty pleasure’ association.

You can have it… but you can’t have too much.

But when we’re talking about ‘not having too much’ - it’s the caffeine that we’re referring to.

Make no mistake, caffeine is a psychoactive drug. It stands to reason we should probably put some boundaries in place here. But other than keeping us awake and maybe making us a bit jittery - how bad is it for us?

In recent years, gut health has become a major topic.

And if you’ve ever had a strong coffee that’s resulted in a quick trip to the bathroom, you’ll be aware that there’s a relationship between coffee and digestion. And not always a harmonious one.

But does that mean it's bad for us?

What’s the relationship between coffee intake, and gut health?

Are we depleting our microbiome with every cup? Or are we doing exactly the opposite?

Fear not coffee lovers, read on...

Key Takeaways

Not got time? Here are the highlights you need to know:

• The gut microbiome is a unique, microscopic ecosystem in our digestive system, influencing digestion, mood, immunity, and overall health.
• A healthy microbiome is diverse, balanced, and functional, with beneficial bacteria like Lactobacillus and Bifidobacterium.
• Coffee is not bad for gut health—in fact, studies show moderate consumption can promote microbiome diversity and feed beneficial bacteria through its polyphenols.
• Decaf coffee offers similar gut health benefits, suggesting caffeine isn’t the main driver.
• To support gut health, focus on a fiber-rich diet, manage stress, stay hydrated, and incorporate prebiotics.
• Prebiotics are fibers found in foods like onions, garlic, asparagus, and chicory root that fuel beneficial bacteria, supporting a balanced and diverse microbiome. Incorporating these foods regularly can help protect and strengthen our gut health.
• For those of us with busy lives, dietary gaps, or limited access to prebiotic-rich foods, Performance Lab® Prebiotic offers a convenient, science-backed solution.
• Performance Lab® Prebiotic contains Orafti® Synergy1, a prebiotic fiber proven to boost Bifidobacterium, supporting microbiome balance, digestion, and inflammation reduction. It’s the ideal companion for maintaining a healthy gut microbiome, especially if your diet or lifestyle falls short.

What Exactly is a Healthy Gut?

Maybe you know about the gut microbiome, maybe you don’t. In a nutshell all of us have a bustling community of trillions of microorganisms—bacteria, fungi, viruses, and more—living in our digestive tract.

It’s like a microscopic ecosystem, working to digest food, produce essential nutrients, protect against harmful invaders, and communicate with your brain and immune system.

Its areas of jurisdiction go beyond just digestion. It influences everything from digestion to mood and immunity—and it’s completely unique to us.

This ‘uniqueness’ means defining a ‘good’ microbiome will vary from person to person.

However, there are some general markers of a healthy microbiome:

• Diversity: A more diverse microbiome is typically associated with better resilience and health.⁽¹⁾
• Balance: The right proportion of beneficial bacteria (like Lactobacillus and Bifidobacterium) relative to potentially harmful ones.
• Functionality: The microbiome should support critical functions, like digesting fiber, producing essential nutrients (e.g., B vitamins and short-chain fatty acids), and modulating the immune system.

It’s this diversity, that holds the key.

Think of it like running a company: these microorganisms all bring a unique set of skills to the table. You need specialists, collaborators, multi-skilled all-rounders, and facilitators. It takes a village—and that’s what your microbiome is.

This microscopic workforce ensures your digestive system runs smoothly—breaking down food, absorbing nutrients, and eliminating waste. A healthy gut microbiome supports the digestive system’s overall efficiency and ensures it works in harmony with the rest of your body.

We must protect it at all costs!

How do we do that? Some of the more obvious ways include regular exercise, eating a healthy diet, reducing our exposure to stress, and getting an adequate amount of sleep. We know those things are good for us.

And whilst we may not know exactly what contributes to our own unique version of a healthy gut, we do know with more certainty what is bad for our gut bacteria:

• Smoking
• Too much alcohol
• Stress
• Lack of dietary prebiotics
• Insufficient sleep
• Antibiotics
• Not consuming a diverse range of foods

But what about coffee? How does our coffee consumption affect our gut microbiome?

Does Coffee Destroy Our Gut Health?

Quite the opposite.

In fact, according to 2024 research⁽²⁾, it may actually enhance it.

Let’s explore what the research says.

Positive Effects of Coffee on the Microbiome

Coffee’s relationship with gut health has been widely studied, and findings suggest several benefits for the gut microbiome:

Coffee Promotes Microbiome Diversity

Research, including data from the large-scale PREDICT studies, has shown that coffee consumption is associated with increased microbiome diversity.⁽³⁾

As mentioned earlier, greater diversity is a marker of a resilient and healthy microbiome. Diversity makes us more capable of adapting to changes and protecting against chronic diseases like obesity and diabetes.

• Dose-Dependent Benefits: These studies revealed that people drinking more than four cups of coffee per day tended to have the highest microbiome diversity compared to non-drinkers or moderate consumers.
• Global Consistency: Data from over 25 countries demonstrated a consistent link between coffee consumption and microbiome diversity, emphasizing its universal benefits.

Coffee Feeds Beneficial Bacteria

Coffee contains polyphenols, a type of antioxidant with prebiotic properties. These compounds fuel beneficial gut microbes, such as Bifidobacterium and Faecalibacterium prausnitzii, promoting their growth and activity. It also supports Lachnospiraceae bacterium A4 and Lactobacillus asaccharolyticus, both strongly associated with coffee drinkers.

Coffee Stimulates Gut Motility

Many coffee drinkers notice its “gut-moving” effects shortly after consumption. This is due to coffee’s ability to:

• Activate contractions in the digestive tract, promoting regular bowel movements.
• Stimulate stomach acid production, aiding digestion and keeping food moving through the gut.

Coffee Contains Antimicrobial Molecules

Certain compounds in coffee can reduce harmful bacteria in the gut, creating space for beneficial microbes to thrive.

For instance, L. asaccharolyticus—a microbe particularly associated with coffee drinkers—has been shown to metabolize coffee’s polyphenols into health-boosting metabolites like hippurate, which improves metabolic and gut health.⁽⁴⁾

Potential Drawbacks

While coffee may boost microbiome health for many people, it’s not without potential downsides:

1. Acidity and Irritation Coffee’s natural acidity can irritate the stomach lining in sensitive individuals, potentially affecting gut pH and the balance of gut bacteria.
2. Impact of Additives Cream, sugar, and artificial sweeteners added to coffee can disrupt the microbiome by feeding harmful bacteria or reducing beneficial species.
3. Overconsumption Excessive coffee consumption (e.g., beyond the recommended 400 mg of caffeine per day) can lead to digestive issues such as diarrhea, heartburn, or discomfort, which might temporarily disturb the microbiome.

What the Research Shows

Studies from organizations like ZOE and others published in Nature Microbiology emphasize that coffee is not only safe for the gut in moderation but may actively support gut health.

In one of the largest studies to date on the relationship between coffee and the microbiome, data was taken from several sources including the ZOE PREDICT studies, The Mind-Body Study and the Men’s Lifestyle Validation Study.^(3,5,6)

Participants were grouped into three categories, those who:

• Never consume coffee: intake was less than 20 grams per day—less than 3 cups per month.
• Moderate consumers: intake was between 21-599 grams per day—up to 3 cups per day.
• High consumers: intake was between 600+ grams per day—more than 3 cups per day.

The results of this study cemented the finding of previous studies, in that there is a strong correlation between coffee and gut diversity. In particular, an increase in L. asaccharolyticus.

L. asaccharolyticus levels were significantly higher in the high consuming group—ranging from 4.5 to 8 times more than in people who never drank coffee.

Similarly, moderate coffee drinkers had 3.4 to 6.4 times more of this bacteria compared to non-drinkers.

This is good news for those who have a moderate intake of coffee.

It means it's possible to reap the benefits of coffee without the jitters, anxiety, and sleep issues that come with a high consumption.

As Dr. Nicola Segata, a leading microbiome expert, explains:

"We noticed that coffee drinkers tend to have higher microbiome diversity, and this diversity increases with the number of cups consumed per day. The relationship seems linked to coffee’s polyphenols and fiber-like compounds, which act as food for beneficial microbes."

Interestingly, the microbiome benefits of coffee—such as increased diversity—were also observed in decaffeinated coffee drinkers, suggesting that caffeine is not the primary driver. There are over a thousand bioactive molecules in coffee. Including vitamin B2, magnesium, and polyphenols.

This is also good news for those who prefer to avoid caffeine altogether. It shows that decaffeinated coffee consumption can offer similar health benefits. You don’t have to rely on caffeine to enjoy what coffee brings to the table.

That said, for those who do consume caffeinated coffee, it’s not just about the complex bioactive compounds—it’s also about the undeniable energy boost, amongst other things...

The Health Benefits of Drinking Coffee

One of the main reasons we drink coffee is for the energy boost.

One of the most profound effects caffeine has, is that it makes us feel less tired, thus increasing our energy levels.

In the brain, caffeine blocks the effects of the neurotransmitter adenosine. This is the brain chemical that makes us feel sleepy, building up throughout the day and easing us into restful slumber come nighttime.

Adenosine sometimes lingers during the morning, which is why it takes us a little time to adjust to daylight and wakefulness.

This is why we opt for a coffee first thing in the morning, helping to diminish the adenosine and block it throughout the day.

Some other coffee benefits (more specifically, caffeine) include:

Caffeine Boosts Metabolic Rate

• Caffeine can increase your resting metabolic rate (RMR), meaning your body burns more calories at rest.
• Studies suggest caffeine can raise metabolic rate by 3-11%, depending on dosage and individual factors.⁽⁷⁾
• Nearly all fat-burning supplements include caffeine because it is one of the few ingredients with consistent evidence of efficacy.
• It also boosts energy and focus, making it easier to maintain exercise intensity and calorie burn.

Caffeine Improves Athletic Performance

• Caffeine stimulates the release of adrenaline, which prepares your body for physical exertion.This leads to increased heart rate, improved blood flow to muscles, and enhanced energy availability.
• By releasing fatty acids from fat stores (lipolysis), caffeine allows the body to use fat as a fuel source, especially during endurance activities. This can help spare glycogen stores, delaying fatigue.
• Studies show caffeine can enhance strength, power, endurance, and overall exercise capacity. Benefits are particularly notable in aerobic activities, but there is evidence of improved anaerobic performance as well.

Coffee Contains Essential Nutrients

These nutrients play a key role in many bodily functions, including energy, muscle function, and brain function.

B-Vitamins: Vitamin B2 (Riboflavin): A cup of coffee provides about 11% of the recommended daily intake (RDI) of riboflavin, which supports energy production and cellular function.

Other B-Vitamins: Smaller amounts of vitamins B3 (niacin) and B5 (pantothenic acid), which aid in metabolism and energy production.

Magnesium: Magnesium plays a key role in muscle contraction, nerve function, and energy metabolism.

Manganese: Manganese is important for bone health, metabolism, and antioxidant functions, and coffee contributes trace amounts.

Potassium: Potassium supports muscle function, heart health, and fluid balance, and coffee provides a small but meaningful amount.

Caffeine May Help You Live Longer

Well, kind of.

Several large observational studies suggest that regular coffee consumption is associated with a reduced risk of premature death. This is because coffee contains bioactive compounds such as antioxidants, polyphenols, and anti-inflammatory agents that may:

• Lower risk of chronic diseases: Coffee drinkers are less likely to develop diseases such as type 2 diabetes, Parkinson's disease, Alzheimer's disease, liver disease, and certain types of cancer.
• Reduced risk of heart disease and stroke: Moderate coffee consumption has been linked to a lower risk of heart disease and stroke in some populations.

Moderation is key here. As are personal factors. Excessive consumption can lead to negative effects such as anxiety, sleep disturbances, or high blood pressure. Genetics, caffeine tolerance, and existing health conditions may affect how beneficial coffee is for each individual.

The Dark Side of Coffee

As with any food or supplement with a shining good side, there are always pitfalls we should consider. Coffee’s benefits are undeniable, but it’s not without its downsides.

However, the negative effects of coffee are largely associated with high intake, so it’s important to find the sweet spot between just enough and too much.

Not for Everyone

Not everyone can tolerate caffeine. Those with heart conditions, who are pregnant, or managing other medical conditions such as irritable bowel syndrome may need to avoid it altogether. Caffeine sensitivity or certain medications can also interact negatively with coffee.

Too Much of a Good Thing

Excessive caffeine consumption can backfire, causing issues that counteract the benefits you’re aiming for when you reach for that morning cup.

If you drink too much caffeine, it can lead to:

• Jitteriness and Anxiety: Overstimulating the central nervous system can leave you feeling on edge, anxious, or unable to focus.
• Insomnia: Drinking coffee too late in the day can interfere with your ability to fall or stay asleep.
• Increased Heart Rate: For some, too much caffeine can cause a racing heartbeat or palpitations.
• Digestive Discomfort: Coffee is acidic and can irritate the stomach lining, leading to heartburn or upset stomach.
• Dependence: Regular overconsumption may result in caffeine dependence, where you rely on it to feel alert and struggle with withdrawal symptoms like headaches and fatigue if you skip your usual dose.

So, how do we know where to draw the line to avoid these effects?

Caffeine: How Much Is Too Much?

Research shows that it is safe to consume up to 400mg of caffeine per day. So, if you stay within this limit, you should be safe.

However, as we have mentioned, everybody is different. Each of us has a slightly different tolerance to caffeine, so it’s important to determine your ideal amount so you can find your personal sweet spot.

Additionally, consuming caffeine after 2 pm is considered a big mistake.

The last thing you want is your afternoon coffee disrupting your nighttime sleep. It takes a fair while for caffeine to exit your system, so be mindful of this if you’re considering a cup of coffee as an afternoon pick-me-up.

While 400mg is the advised recommendation, athletes are usually recommended higher doses to improve physical performance. Keep in mind that these recommendations are relative to bodyweight and should only be followed by those who are in tune with their personal tolerance.

How to Help Rebalance Your Gut

Whether you’re a coffee lover or just looking to keep your microbiome in peak condition, there are practical ways we can rebalance and support our gut health:

1. Prioritize Fiber-Rich Foods

• Fiber is essential for gut health, acting as food for beneficial bacteria. Aim to include:
• Fruits like apples, berries, and bananas.
• Vegetables such as broccoli, spinach, and artichokes.
• Whole grains like oats, quinoa, and brown rice.
• If you drink coffee, pairing it with fiber-rich foods can help maintain balance and fuel your microbiome.

2. Hydrate Consistently

• Coffee is a mild diuretic, so ensure you’re drinking enough water throughout the day to prevent dehydration and support digestion.

3. Limit Additives in Your Coffee

• Sugar, creamers, and artificial sweeteners can disrupt the gut microbiome. Opt for black coffee or alternatives like unsweetened almond milk if you’re looking to protect your gut.

4. Consume Coffee in Moderation

• Stick to the recommended daily limit of 3–4 cups (or up to 400 mg of caffeine) to enjoy the benefits without overwhelming your digestive system.
• If you experience digestive discomfort, consider switching to decaf or consuming coffee earlier in the day.

5. Diversify Your Diet

• A diverse diet leads to a more diverse microbiome, which is associated with better gut health. Aim for a variety of fruits, vegetables, proteins, and healthy fats.

6. Manage Stress

• Chronic stress can disrupt the microbiome, so incorporating stress-reducing activities like yoga, meditation, or regular exercise can help maintain balance.

7. Be Mindful of Antibiotics

• Antibiotics can disrupt gut bacteria by killing off both harmful and beneficial microbes. After a course of antibiotics, consider replenishing your gut with probiotics and prebiotic-rich foods.

8. Incorporate Probiotics and Prebiotics

• Probiotics: Live bacteria that can replenish your gut microbiome. Consider fermented foods like yogurt, kefir, sauerkraut, kimchi, or a high-quality probiotic supplement.
• Prebiotics: These are non-digestible fibers that feed beneficial bacteria. Sources include onions, garlic, asparagus, and prebiotic supplements.

The Best Prebiotic For a Healthy Gut

Whilst probiotics introduce new strains of bacteria into our gut, prebiotics are fuel for the good ones that already inhabit our microbiome.

Performance Lab® Prebiotic, features Orafti® Synergy1, which has been shown in human research to shift Bifidobacterium distribution in the gut from 20% to 71%.

Why is this important?

Because Bifidobacterium has been linked to studies showing it may:

• Improve symptoms of irritable bowel syndrome.
• Reduce inflammation in people with inflammatory bowel disease
• Lower blood cholesterol
• Support the growth of beneficial bacteria whilst inhibiting the growth of harmful pathogens.
• Restore microbiome balance disrupted by illness, poor diet and antibiotics.

Performance Lab Prebiotic delivers more reliable, natural, safe, and comfortable microbiome support.

Shop Performance Lab® Prebiotic

Summary

The verdict is in: When consumed in moderation, coffee supports gut health rather than harming it.

Its polyphenols promote diversity in the microbiome, feeding beneficial bacteria and boosting resilience against chronic diseases.

Even decaf coffee provides these benefits.

It’s always a good idea to assess your personal tolerance to caffeine, as well as the effects it has on your sleep, mood and stomach.

Your gut is the key to your overall wellbeing. So nourish it with prebiotic-rich foods like onions, garlic, and asparagus to fuel beneficial bacteria and maintain microbiome balance.

For those needing a little help looking after their gut, start with prebiotics. This will nourish the beneficial bacteria that already exists in our microbiome.
If you’re a coffee lover seeking better digestive health, combining good habits with targeted support can help you maintain a thriving microbiome.