Coffee and Digestion: 8 Digestive Problems with Coffee

After doing the research for this post, 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, coffee tasting substitute I’ll share ahead. 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 this legal drug than we’d like to admit to ourselves.

What I hope to offer with this post is some motivation and momentum to give up coffee. I’ll do this by covering the damaging effects it can have on your gastrointestinal tract and the way these side effects lead to various health issues and digestion problems, including stomach pain, bloating, intestinal cramps, diarrhea and excessive gas.

And for some good news, in following posts I’ll go into some of the best ways to beat a caffeine addiction by replacing coffee with healthier alternatives. Just making this one change in your drinking habits could make a dramatic difference to your health and sense of well being in your daily life.

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

8 Negative Side Effects of Coffee and Caffeine

1. Coffee Increases Stomach Acid 

Coffee contains various acids, oils and chemical compounds like caffeine that can harm your stomach and intestines by irritating their linings. When you drink coffee your stomach produces large amounts of hydrochloric acid (HCl).

This overproduction of HCl is especially pronounced if you drink a cup of coffee on an empty stomach, making first thing in the morning probably the worst possible time to drink coffee if stomach pain is a problem for you.

Your body can 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.How coffee causes gas

2. Coffee Causes Gas

When there is a shortage of hydrochloric acid for digestion you often have problems digesting protein in particular.

This is one of the main ways coffee causes gas as undigested, putrefying protein is feed on by the intestinal bacteria that create hydrogen sulfide (rotten egg gas) 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 bloating and intestinal cramps soon after drinking coffee, even diarrhea in extreme cases.

By interfering with proper digestive processes, coffee 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 coffee 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 excessive gas by diverting your body’s resources away from proper digestion and into ‘fight or flight’ mode.

All in all there’s quite a few ways that coffee can cause stomach pain, intestinal cramps, bloating and bad gas as it can potentially interfere with digestion throughout all of its various stages.

3. Stomach Pain, Heartburn & Indigestion

Coffee can cause stomach pain and heartburn (acid reflux) by relaxing the lower esophageal sphincter muscle. This important 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 and causing acid reflux, often identified as an upset stomach or indigestion.

Caffeine is known to have a relaxant effect on the lower esophageal sphincter muscle but the problem has been shown to occur even with decaffeinated coffee. So it seems other compounds, like the various organic acids in coffee, can also be responsible for the stomach pain many people experience when they drink it.

In fact, apart from minimizing the jittery, fight or flight response from the caffeine, decaf does not seem to fare much better in the health stakes than regular coffee.

It has most of the same irritating oils, acids and compounds, the same diuretic, laxative and mineral blocking effects and has actually 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 somebody looking to let go of their addiction, but it’s not a long-term solution if you value your health.

This non-acidic, caffeine-free and digestive healthy Teeccino is the best coffee tasting replacement I’ve found. It brews up like regular java but its organic ingredients would not interfere with digestion or cause flatulence.

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 actually use coffee deliberately as a laxative and it can indeed stimulate the process of peristalsis that sends us to the bathroom. The laxative effect of coffee is so strong it has been observed only 4 minutes after drinking it.

The problem is, hand and hand with this process, coffee also appears to stimulate gastric emptying of the stomach before food has a chance to be properly broken down.

The acidic stomach contents are dumped into the small intestine too early and may cause injury or inflammation to the very place that is supposed to be absorbing nutrients to keep you alive and healthy. More undigested food also usually equals more problems with bloating and gas.

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

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

5. Ulcers and IBS

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

In fact, while ulcers are believed 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 an intestinal irritant for anyone suffering gastrointestinal problems like stomach cramps, belly bloating and irritable bowel syndrome.

It’s not the caffeine that is as much of a problem as certain enzymes in the coffee beans themselves. This is why switching to decaf for IBS or ulcer 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 all forms of coffee need to be avoided if you have a stomach ulcer, IBS or ongoing intestinal pain.

The caffeine in coffee is a strong diuretic in the human body. In large doses it can increase fluid flushing through the kidneys which leads to a frequent need to pee, loss of minerals and other important nutrients and dehydration.

Dehydration may actually lead to weight gain in a roundabout way. When we are dehydrated the body has a strong need to replenish water but our brains often seem to mistake this signal for the feeling of being hungry. So we reach for a snack (often a salt laden one, making dehydration even worse) when what we really need is more water.

The next time you feel like you need a snack outside of normal meals, try to drink water first. There’s a fair chance you’re just dehydrated and drinking water will lessen your hunger.

7. Affects Mineral Absorption

Drinking coffee may restrict our kidneys ability to retain magnesium, calcium, zinc and other important minerals. Iron absorption in the stomach can 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 worrying digestion wise as it is needed to maintain bowel regularity and prevent constipation. And constipation is a common cause of smelly gas, so here is yet another way coffee can make you fart.

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

If you suspect are not getting enough magnesium (or drinking coffee has inhibited its absorption), 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.

8. Elevates Stress Levels and Interferes with GABA Metabolism

Coffee elevates the stress hormones cortisol, norepinephrine and epinephrine (adrenaline) that increase heart rate, blood pressure and activate the body’s ‘fight or flight’ response.

Hormones like adrenaline are supposed to trigger when we are in danger and need to respond quickly. They are not meant to be ‘on’ all the time in the way drinking coffee can make them. Is that jittery rush caffeine gives us really energy? Wouldn’t a better word for it be anxiety?

This increase in stress hormones can also inhibit the process of digestion, particularly in the stomach. This is due to the way the body takes blood and resources away from the digestive processes in preparation for a potential threat. A threat that never comes (though indigestion, bloating and flatulence problems may well).

Coffee and the caffeine in it also play havoc with the metabolism of gamma-aminobutyric acid (GABA). GABA is found in both your brain and your intestines. In the brain, GABA plays an important role in regulating mood and stress management. In the gastrointestinal tract, GABA provides a calming effect on the whole system.

Both of these functions are important for healthy digestion and indeed overall health and well being. Unfortunately, caffeine interferes with the way GABA binds to its receptors to provide that calming influence on both the brain and the GI tract (Ever tried slowing down and being very calm after a strong cup of java?).

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 relaxation and stress management.

Last Thoughts on Coffee and Digestion

I am well aware there are many people out there who won’t want to hear all of these bad things written about their good friend coffee. But it’s worth asking yourself, what kind of friend does this kind of damage to your digestion and your health in general?

Caffeine addiction is a very common problem in Western societies. Aside from well known issues with heightened stress and sleeping disorders, much fewer people know about digestive problems from coffee like an upset stomach, belly bloat and excessive gas.

Can you get away with a cup or two a day without obvious issues? Maybe. But then again, anyone reading a website on flatulence and gastrointestinal problems is probably aware that they have an issue or two, even if it’s not that obvious yet.

Wouldn’t it be better to address some of the causes of those digestive issues 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.

Actually, giving up coffee doesn’t have to be that big a deal. Substituting it with something refreshing that gives a better type of energy, like peppermint tea 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 a bunch of great alternatives (this one even tastes like coffee but is alkaline rather than acidic and actually quite healthy).

Following on from there is a detailed plan for coffee replacement with specific steps for minimizing withdrawal to help you give up coffee easily and permanently for better digestion and a calmer and healthier life.

Photo: bradleypjohnson

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Click Here to Leave a Comment Below 6 comments
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.


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,


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.


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?



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

All the best,



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

All the best,



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