Is Coffee Bad for Your Gut? Debunking Myths & Eliminating Your Fears About Coffee

Key Points:

  • Is coffee bad for your gut? Probably not. If your gut is already sensitive, then you might experience symptoms from your morning cup of joe (think an impromptu bathroom run). But in general, drinking coffee is known to decrease mortality rates and provide nutritional benefits.
  • While coffee itself isn’t bad for you, some coffee beans are contaminated by pesticides and mycotoxins that can drastically impact your gut and immune system. Prioritize organic coffee that’s tested for mycotoxins and mold. If you’re buying decaf, make sure it’s water-processed instead of chemical-processed.
  • There are so many ways to optimize your morning coffee, and “drink up” the many benefits it provides. Use cream or milk to neutralize the acidity of your coffee, add healthy fats like BodyBio Balance Oil to blunt the caffeine high, drink it with or after a healthy breakfast, and make sure your nervous system is relaxed before indulging.

Maybe you clicked on this blog with shaking hands. What if they tell me my beloved coffee is destroying my gut health?

Good news: We’re not here to take away anyone’s daily cup of joy and motivation.

But let’s face it, there’s a lot of conflicting information about coffee and gut health. Your favorite wellness guru on Instagram says it’s draining your body of essential minerals — while the medical studies have something entirely different to say (seriously, they link it to significantly lower all-cause mortality rates).

We side with the science and what seems to be far more pros than cons — we’re not going to tell you to stop drinking coffee. But we are going to tell you how to drink it better.

One reason there’s so much conflicting information about coffee is because the quality, origin, and quantity of your coffee directly impact how it makes you feel — and how it impacts your gut health.

Let’s explore coffee and gut health — its impact on gut flora, digestion, oxidative stress, and beyond.

Table of Contents:

Coffee and Gut Health — The Benefits of Coffee

Clever marketing is constantly trying to sell you the latest and greatest superfoods. But what if you’re already consuming a powerful superfood every morning? Yep, it’s coffee.

Seriously, coffee is packed full of antioxidants. It also has a number of vitamins and minerals, like magnesium and vitamin B. In studies, it’s shown to protect against diseases like Alzheimer's disease, liver disease, and cardiovascular disease.

Coffee is even known to change the microbiome — for the better. One study found that individuals who drink coffee have higher rates of an anti-inflammatory microbiome (more Bifidobacterium, to be exact).

Why Does Coffee Upset My Stomach?

When it comes to coffee and gut health, those with a sensitive stomach or other underlying issues may suffer from digestive complaints when consuming too much.

Caffeine itself does increase muscle contractions in the digestive system — meaning it stimulates the digestive tract to get moving. If your iced coffee prompts more than one bathroom trip, it’s best to target your digestive health in other ways and possibly ease up on the coffee intake (or try decaf).

Coffee is also pretty acidic, so people who struggle with acid reflux could feel increased symptoms when drinking their morning cup of joe.

One solution is to try adding whole milk or cream to your coffee cup. The fat and protein content slows the release of caffeine, meaning slower digestive tract contractions. The benefit of whole milk is that it’s alkaline, too, so it eases the acidic stress. Coconut milk, collagen powder, and MCT oil are good additions for those who can’t handle dairy.

If coffee consumption causes regular digestive issues, you don’t have to stop drinking it entirely. But you should create healthy boundaries with coffee and find better ways for your body to consume it. And you should definitely aim to improve your gut health with supplements and lifestyle changes.

Coffee Do’s and Don’ts for Better Gut Health

For most people, coffee is a life staple and a comforting habit that helps motivate you to get your day started. We’re not joy-stealers — and we’re not going to tell you to stop drinking coffee. However, if you struggle with gut dysbiosis or a chronic health issue, there are a few potential risks to consider when consuming the world’s favorite beverage.

These are our coffee do’s and don’ts. They’ll act as a guide to help you understand how your body processes coffee, and how to protect your gut. Most likely, you’ll be less jittery, more energized, and exhibit fewer gut symptoms when enjoying coffee alongside these principles.

1. Don’t Drink Coffee on an Empty Stomach

Coffee is pretty acidic, so consuming it on an empty stomach before breakfast can shock the gut and increase acid reflux symptoms first thing in the morning. It also acts as an appetite suppressant, which might mess up your circadian rhythm first thing in the morning and could motivate you to skip breakfast.

Instead, we recommend drinking coffee alongside a nutritious breakfast, and after at least one 16 oz. glass of water. Other nutrients, especially fats and protein, can slow the release of caffeine. This helps to eliminate acid reflux symptoms and ensures you get enough food to energize your morning (seriously, a healthy breakfast is vital for hormone balance, especially in women).

2. Don’t Drink Coffee Too Early

Exposure to natural light in the morning plays a crucial role in regulating our body's internal clock, or circadian rhythm, which in turn influences numerous physiological processes including the secretion of hormones like melatonin. Drinking coffee, which contains the stimulant caffeine, can impact adenosine receptors in the brain. Adenosine is a neurotransmitter involved in promoting sleep and relaxation. When caffeine blocks its receptors, feelings of wakefulness are promoted.

By waiting to consume coffee until after one has been exposed to natural light, individuals can ensure that they're not prematurely or unnecessarily altering their adenosine function. This allows for the body to wake up more naturally and in sync with its circadian rhythm, and can potentially lead to better sleep quality and overall health in the long run.

3. Don’t Drink Caffeinated Coffee If You Have High Cortisol (Try Decaf Instead)

Sadly, high cortisol is a reason to skip your morning cup of coffee. If your body is already buzzed on cortisol and adrenaline, caffeine is just one more contributing factor to unstable energy and imbalanced hormones.

Focus on tools like somatic exercises, EFT tapping, box breathing, and yoga to get your body out of constant fight or flight. Once your body spends most of its time in the parasympathetic nervous system, you can gently add caffeine back into your routine. In the meantime, try water-processed decaf or switch to non-caffeinated tea.

4. Don’t Drink Coffee with Pesticides and Contaminants

Coffee is a huge industry — and it’s one of the biggest offenders for pesticides. If you’re avoiding gluten, oats, pasta, and other foods due to potential glyphosate contamination, you really should be looking at your coffee too. The best way to ensure your morning coffee is not contributing to toxic burden? Buy organic. There are even some brands that are certified glyphosate-free.

5. Don’t Drink Coffee with Mycotoxins

Mycotoxins are a chemical compound released by toxic mold — and they deserve their own category. Essentially, mycotoxins are the elements of mold that make you sick (and usually have to filter through the liver). Due to poor processing, storage, and environmental factors, a lot of conventional coffee brands contain mycotoxins.

If you have a sensitive gut, we recommend you find an organic coffee brand that tests often for mycotoxin and pesticide contamination.

6. Don’t Use Coffee to Cover Up Underlying Fatigue

If you haven’t pulled an all-nighter fueled on coffee and determination alone, then have you really lived? But in all seriousness, coffee shouldn’t be used as a crutch to get through constant fatigue. While it offers a great energy boost for the morning, it’s a bad sign if you’re using coffee to mask feelings of fatigue on a regular basis.

Instead, ease off the coffee and focus on hormone balancing, circadian rhythm, gut health, and natural detox.

7. Do Enjoy a Dopamine Boost

If your morning java makes you happy, it might be because it raises neurotransmitters (specifically dopamine) in the brain. This is a great way to get neurotransmitters firing early in the morning — and could be a natural intervention to help fight against depression. For best results, pair it with other dopamine-boosting activities, like early morning sunshine, exercise, and meditation.

8. Do Drink Water-Processed Decaf

If you’re taking a break from caffeine for health reasons, make sure you drink water-processed and organic decaf coffee. Most coffee brands use chemicals to remove caffeine from your packaged coffee — which adds even more contaminants to a product that’s already flagged for mycotoxins and high pesticide levels. A water-processed decaf coffee is a much safer choice.

9. Do Limit Yourself to 2-4 Cups Daily

If you’re in perfect health and don’t have high cortisol, two to four cups of coffee per day seems optimal, according to studies. Any more than this is toeing the line for nervous system and circadian rhythm disturbance.

BodyBio Tip: Never use alternatives like caffeinated pills or energy drinks. These aren’t the same as coffee and can have adverse effects on your cardiovascular health. Espresso is fine to drink, but keep in mind one shot is about the same as a full twelve-ounce cup of coffee.

10. Do Regularly Evaluate How Coffee Makes You Feel

Regularly checking in with your body is one of the best ways to ensure you aren’t crossing boundaries with food and drinks. If coffee is adversely impacting your nervous system, you’ll feel it. If heartburn and gut dysbiosis are making coffee consumption uncomfortable, your body will alert you with symptoms — it’s your job to pay attention and react accordingly.

Check in with your body regularly and don’t be afraid to make adjustments as needed.

If Your Gut Is Struggling, It’s Probably Not the Coffee

Here’s the thing: Coffee has so many incredible health benefits. But it shouldn’t be used as a crutch to boost gut motility and fight constant fatigue. If you’re struggling to use the bathroom without your morning cup of joe (or alternatively, if you have to run to the toilet after just a few sips) it’s time to take a closer look at your gut health.

Our Butyrate supplement promotes a healthy microbiome and cultivates an environment where digestion is easy, uncomplicated, and doesn’t require an extra caffeinated nudge.

Don’t Give Up Your Coffee — Try Butyrate


Poole, R., Kennedy, O. J., Roderick, P., Fallowfield, J. A., Hayes, P. C., & Parkes, J. (2017). Coffee consumption and health: umbrella review of meta-analyses of multiple health outcomes. BMJ (Clinical research ed.), 359, j5024.

Yashin, A., Yashin, Y., Wang, J. Y., & Nemzer, B. (2013). Antioxidant and Antiradical Activity of Coffee. Antioxidants (Basel, Switzerland), 2(4), 230–245.

Dai, A., Hoffman, K., Xu, A. A., Gurwara, S., White, D. L., Kanwal, F., Jang, A., et al. (2023). The Association between Caffeine Intake and the Colonic Mucosa-Associated Gut Microbiota in Humans—A Preliminary Investigation. Nutrients, 15(7), 1747. MDPI AG.

Merhi, A., Kordahi, R., & Hassan, H. F. (2022). A review on the pesticides in coffee: Usage, health effects, detection, and mitigation. Frontiers in public health, 10, 1004570.

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