8 Ways Coffee Damages Digestion and Makes You Gassy

Java closeupAfter doing the research for this article I gave up coffee. I’m done with it.

I took the last I had to work as an offering to the caffeine addicts there and replaced it with a caffeine-free yet similar tasting substitute. It was actually easier than I’d expected.

Giving up their daily caffeine fix is a scary thought for some people. Many of us are far more addicted to it than we’d like to admit to ourselves.

What I hope to offer with this post is some positive motivation and momentum to stop drinking coffee easily and permanently.

I’ll do this by covering the damaging effects it can have on your digestive system. As well as symptoms and side effects, including stomach pain, bloating, intestinal cramps, diarrhea and excessive gas.

And for some good news, in following articles I’ll cover caffeine withdrawal remedies, replacing it with healthier alternatives and a step by step plan to quit.

Just making this one change in your drinking habits can make a dramatic difference to your digestive health and sense of calmness and wellbeing in your daily life.

Okay, if you’ve made it this far without being scared off then let’s get started.

8 Digestive Side Effects of Coffee and Caffeine

1. Increases Stomach Acid 

Coffee contains many acids, oils and chemical compounds like caffeine that can harm your stomach and intestines by irritating their linings. When you drink it your stomach increases gastric secretions of hydrochloric acid (HCl) in reaction to these oils and acids.

This effect is especially pronounced if you drink it on an empty stomach. That makes first thing in the morning the worst time to drink coffee if stomach pain is a problem for you.

Your body has a limited ability to make hydrochloric acid, particularly if you are dehydrated, nutritionally deficient or under stress.

By drinking regular cups of coffee you are kicking stomach acid production into overdrive. Do this for long enough and your body’s capacity to produce hydrochloric acid can be impaired.

2. Coffee Causes Gas

When there is a shortage of hydrochloric acid for proper digestion, your body has problems breaking down protein in the upper intestine. This is one of the main reasons coffee causes bad gas.

This protein passes largely undigested into the lower intestine. Here it putrefies as it is feed on intestinal bacteria. As a byproduct of this process they create gases like hydrogen sulfide (rotten egg gas), responsible for those really smelly farts.

Another way coffee makes you gassy and bloated is by stimulating gastric emptying when you drink it with or soon after a meal.

By causing the contents of your stomach to evacuate before gastric processes have done their usual job, digesting food arrives into your small intestine too early. This can cause abdominal bloating, intestinal cramps and even diarrhea in extreme cases.Caffeinated drink

It can also make you fart many hours later, when poorly broken down food arrives in your lower intestine to feed flatulence-causing bacteria.

Most people wouldn’t recognize their morning java as a prime suspect in why they are so gassy in the afternoon or evening.

Even the way coffee elevates cortisol and adrenaline to give you energy (or is that anxiety) can be responsible for bloating and gassiness. This is due to the way it diverts your body’s resources away from digestion and into ‘fight or flight’ mode.

All in all, there’s many ways that coffee can cause gas since it can interfere with multiple stages of the digestive process.

3. Causes Indigestion and Heartburn

Drinking coffee can be responsible for heartburn (acid reflux) by relaxing the lower esophageal sphincter muscle. This muscle separates your sensitive esophagus from your stomach with its hydrochloric acid.

It acts as a valve that should stay tightly closed to prevent gastric secretions from backing up into the esophagus. When this process isn’t working properly the result is acid reflux, often identified as an upset stomach or indigestion.

Caffeine is known to have a relaxant effect on the lower esophageal sphincter muscle. The problem has been shown to occur even with decaffeinated coffee though.

In fact, apart from minimizing cortisol production from caffeine, decaf does not appear to be much better for digestive health than regular coffee.

It has most of the same irritating oils, acids and compounds, the same diuretic, laxative and mineral-blocking effects, and has been shown to be even more acid-forming in the gastrointestinal tract than regular coffee.

Decaf may have a temporary role in giving up coffee for some people looking to let go of their addiction, but it’s not a long-term healthy solution.

Non-acidic and caffeine-free Teeccino is the best tasting replacement I’ve found. It brews up like regular java but its organic ingredients do not interfere with digestion.

If coffee is giving you an upset stomach and making you gassy then try switching to this much healthier alternative.

4. Laxative Effects and Diarrhea

Some people use coffee deliberately as a laxative and it can indeed stimulate the process of peristalsis that sends you to the bathroom.

In fact, this laxative effect is so strong it has been observed in studies to happen only 4 minutes after drinking it.

The problem is, hand in hand with this process, coffee also stimulates gastric emptying of your stomach, often before food has a chance to be properly broken down.

When acidic stomach contents are dumped into the small intestine too early, it can result in injury or inflammation to the very place that is supposed to be absorbing nutrients.Caffeinated beverages

Food that is poorly broken down in the stomach will also remain only partially digested in the small intestine. Once it reaches your lower intestine that equals more problems with bloating and farting.

For sensitive people, coffee can even cause diarrhea if its gastric emptying properties kick in at the wrong time. Drinking milk with it will also exacerbate the risk of diarrhea due to its gas-causing lactose.

Decaffeinated coffee has been shown to have the same laxative effects so researchers don’t think caffeine is solely responsible. Another mark against decaf for digestive problems unfortunately.

5. Ulcers and IBS

Coffee is a well-known gastrointestinal irritant for those suffering from IBS, gastritis, Crohn’s, colitis and ulcers and most GPs recommend it be avoided for sufferers.

In fact, while ulcers are known to originate from the Helicobacter pylori bacteria, coffee’s acidic effect on the stomach can provide suitable conditions for the bacteria to access the stomach lining in the first place.

Coffee is often cited as problematic for anyone suffering from the symptoms of irritable bowel syndrome. While caffeine can cause problems, certain enzymes in the beans also have negative effects. This is why switching to decaf for IBS sufferers rarely works.

Regular exposure to coffee’s acidity can also prevent the healing of an already damaged GI tract. Once again, regular or decaffeinated makes no difference in this regard so both need to be avoided if you have a stomach ulcer, IBS or ongoing intestinal pain.

7. Affects Mineral Absorption

Drinking coffee can restrict your kidney’s ability to retain magnesium, calcium, zinc and other important minerals.

Iron absorption in the stomach is also be heavily impaired if coffee is taken at the same time as an iron-rich meal. All of these minerals are required in the complex process of digestion at some point.

Reduction in the already hard to get magnesium is especially bad as it is needed to prevent constipation and maintain bowel regularity. With constipation a common cause of smelly gas, this is yet another way coffee can make you fart.

Many people are deficient in essential magnesium but unfortunately it is poorly absorbed in multivitamins and other supplements.

If you suspect are not getting enough of this mineral then transdermal magnesium oil, sprayed directly onto your skin after a shower, can help replenish your body’s magnesium stores. I have personally noticed a real reduction in muscle tension and an improvement in my energy levels since using it.Brewed java

8. Caffeine Elevates Stress Levels and Interferes with GABA Metabolism

Drinking caffeinated beverages elevates the stress chemicals cortisol, norepinephrine and epinephrine (adrenaline) that increase heart rate, blood pressure and activate your body’s ‘fight or flight’ response.

Adrenaline is supposed to trigger when you are in danger and need to respond quickly. It’s not meant to be ‘on’ all the time in the way drinking coffee can make it.

Is that jittery rush caffeine gives you really a good form of energy? Wouldn’t a better word for it be anxiety?

This increase in stress hormones can also inhibit the entire process of digestion. This is due to resources being taken away from gastrointestinal processes in preparation for a potential threat.

Coffee and the caffeine in it also play havoc with the metabolism of gamma-aminobutyric acid. GABA is an important neurotransmitter found in both your brain and your intestines.

In your brain, GABA plays an vital role in regulating mood and stress management. While in your gastrointestinal tract it provides a calming effect and keeps things moving along.

Caffeine interferes with the way GABA binds to its receptors to provide that calming influence on both the brain and the GI tract. This can both elevate anxiety and damage digestion.

As a final parting shot to your stress levels, coffee can also cause an increase in the excretion of B vitamins, which are central to both relaxation and mood management.Empty cup of Joe

Caffeine Addiction and Digestive Function

Many people won’t want to hear all of these negative things written about their good friend coffee. It’s worth asking though, what kind of friend would do this much damage to your digestion and by extension your overall wellness and wellbeing?

Caffeine addiction is a very common problem in Western societies. Aside from well known issues with heightened stress and sleeping disorders, far fewer people know about the many digestive problems caused by coffee.

Can you get away with a cup or two a day without obvious issues? Maybe.

But then again, anyone reading a website like this one is probably aware that they have some digestion problems.

Wouldn’t it be better to address some of the causes of those digestive symptoms before they become even more obvious and less easy to deal with?

Besides, if you’re not addicted to coffee, then it can’t hurt to replace it with a healthier alternative for a couple of weeks and see whether problems like stomach pain, diarrhea, bloating and farting are reduced.

Better Alternatives and a Replacement Plan

Giving up coffee doesn’t have to be that big a deal if you do it properly.

Substituting it with something refreshing that gives a better type of energy, like peppermint or ginger tea, while using these caffeine withdrawal remedies, can help you get through the first few days. It’s usually pretty smooth sailing after that.

The next page has 3 steps to replacing coffee and 5 different alternatives (one even tastes very similar but is alkaline rather than acidic and quite healthy).

Following on from there is a detailed plan to it give up, with specific steps for minimizing withdrawal symptoms. Anyone can use it to quit coffee easily and permanently for better digestion and a calmer and healthier life.

Click Here to Leave a Comment Below 9 comments

I took a middle-road approach: When this post appeared, I started to gradually make my coffee weaker over a 2-month period. I’m presently drinking coffee that’s 1/4 strength. I do the same thing at work and home, and I simply don’t drink coffee anywhere else.

My taste buds adapted, so I still get to enjoy my weakened coffee. My stomach and digestion are much happier.

I do now drink about 2x the volume of coffee, but it’s over a much longer time period, and is still half the caffeine I used to take in. And my coffee supply lasts twice as long.

    James Dillan

    Hi Bob and thanks for your comments. Glad your digestive system is feeling better.

    This slow reduction approach could work well for people who can’t imagine not drinking coffee but know they need to reduce their intake.

    All the best,



thankyou for sharing the valuable information. yes, this is true caffeine is the cause of stomach ulcers and all stomach problems.


Thanks for the right up. I too is suffering from the symptoms you mentioned here. I finally gave up coffee today and would like to try the teas you suggested. How long did it take for you to have those symptoms go away? Was it instantaneous or did it take a few days or even weeks?


    James Dillan

    Hi Frank,

    Usually the next day you should feel a bit better and your digestive system should improve over the next couple of weeks if coffee was the primary irritant.

    Be aware that if you were drinking your coffee with milk it could also be causing digestive problems https://flatulencecures.com/lactose-sensitivity-why-milk-causes-gas/

    All the best,


Robert McLoughlin

Having survived obstructive jaundice and pancreatic cancer so far, I’ve been told to avoid alcohol and have never smoked. Now I am being told to avoid one of my few remaining pleasures: coffee. But reading the affects of coffee, flatulence, loose stools, are very familiar to me.

    James Dillan

    Hi Robert,

    I do apologise for being the bearer of bad news on coffee.

    I’d recommend trying the coffee replacement Teeccino suggested in this article for a similar tasting alternative that won’t cause you these digestive problems https://flatulencecures.com/replace-coffee/

    All the best,


Zacharia Aboulkhair

Thank you so much for this much informative article. I have basically given up coffee except for an occasional Sunday brunch with my family. This particular Sunday I treated my self to a coffee with brunch, and feel awful. It has been a couple weeks since drinking coffee and everytime I indulge I experience everything your article has talked about. Today I came across your article and would just like to thank you again. I am absolutely done with coffee after reading and no longer in the denial you talk of.

    James Dillan

    Hi Zacharia and thanks for your comment.

    While the negative effects of coffee aren’t well covered online, it’s clear to me that many people have problems with it yet aren’t aware it’s the culprit of their symptoms. It’s good you were able to identify it and give it up.

    All the best,



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