Does Coffee Harm Your Gut?

by Dr. Edward Group DC, NP, DACBN, DCBCN, DABFM
Published on , Last Updated on

A table full of coffee beans. Coffee reduces absorption of the nutrients, which can bad for the gut.

Coffee’s received a lot of good publicity in recent years for the way it appears to protect the brain from degenerative diseases. We know that coffee is full of antioxidants, vitamins, minerals, amino acids, plant-compounds, fats, and carbs. In small amounts, coffee can actually be beneficial for most healthy individuals. The main downside to coffee is that it’s highly acidic, and this acidity can have possible repercussions on the gut.

Coffee’s Effects on the Gut

Before you drink your next cup of java, weekend latte, or morning cup of joe, here’s five facts to know about coffee’s effect on the gut.

1. Higher Stomach Acidity

Drink a lot of coffee first thing in the morning on a regular basis, and gut problems may be right around the corner. It’s not just the caffeine that does this, so drinking decaf won’t avoid the danger. Caffeine and other plant-based compounds stimulate the stomach cells to release more hydrochloric acid, which can, at times, aid digestion.[1, 2] But regular coffee drinking, especially in the morning on an empty stomach, reduces the amount of stomach acid available for digestion later on. H. pylori bacteria, the main bacteria responsible for ulcers, prefers highly acidic environments. Combine this with the way coffee weakens the protective barrier of the stomach – the mucosal layer[3] — and the risk of damage and ulcers increases.

2. Encourages Acid Reflux

Drink enough coffee and you may experience acid reflux or heartburn. Coffee relaxes the esophageal sphincter—the gatekeeping muscle valve that allows food into the stomach and makes sure it stays there. Stomach acid that escapes irritates the tissue of the esophagus. If it happens frequently enough, complications like sores, ulcers, or permanent changes to cells in the esophagus can occur.

3. Aggravates IBS and Other Bowel Disorders

Coffee intensifies symptoms of bowel conditions like gastritis, irritable bowel disorder, colitis, and Crohn’s Disease. Certain enzymes in coffee trigger an immune response that results in inflammation, bloating, cramping, gas, and diarrhea.[4]

4. Raises the Chance of Food Rotting in the Gut

Coffee’s known to encourage the stomach to release its contents into the small intestine before complete digestion has occurred.[5] Food that doesn’t get fully digested often ends up sitting and rotting in the gut. This creates a toxic environment ideal for ‘bad’ bacteria to spread in the intestines, damages the intestinal wall, and leads to inflammation and an immune response to enzymes in the coffee.

5. Over Stimulates Intestinal Wave Action

Nerve and brain cells rely on a neurochemical called GABA. It’s responsible for calming the nerves after they fire. The caffeine in coffee prevents GABA from doing its job and this may lead to overactive bowels. The most common symptom is cramping or an urge to go to the bathroom.

One Final Thought

While it doesn’t directly harm the bowels, coffee does reduce the retention and absorption of minerals like magnesium, calcium, zinc, and iron. Here’s a basic rundown on these nutrients:

  • Magnesium keeps the muscles relaxed and firing correctly.
  • Calcium is needed for strong bones and getting cells the nutrients they need.
  • Zinc fuels the immune system.
  • Iron’s essential for creating new red blood cells.

And you should not drink coffee if you have gallstones. Coffee doesn’t cause gallstones, but it does cause the gallbladder to contract, creating a very painful situation. When it comes to coffee, the best way to know if harm’s being done is to notice how you feel. If it has a severe laxative effect or causes cramping or acid reflux, you may want to take some time off. Studies have shown the damage and irritation quickly heals once coffee consumption stops.

Are you a coffee lover? Or do you avoid the stuff like plague? Share your experience with us below.

References (5)
  1. Börger HW, Schafmayer A, Arnold R, Becker HD, Creutzfeldt W. The influence of coffee and caffeine on gastrin and acid secretion in man (author's transl). Dtsch Med Wochenschr. 1976 Mar 19;101(12):455-7.
  2. Kuz'menko LI, Bohdanova OV, Ostapchenko LI. Regulation of secretory processes in parietal cells in the different stomach pathologies. Ukr Biokhim Zh. 2006 Jul-Aug;78(4):80-8.
  3. Cibicková E, Cibicek N, Zd'ánský P, Kohout P. The impairment of gastroduodenal mucosal barrier by coffee. Acta Medica (Hradec Kralove). 2004;47(4):273-5.
  4. Sauer T, Raithel M, Kressel J, Muscat S, Münch G, Pischetsrieder M. Nuclear translocation of NF-?B in intact human gut tissue upon stimulation with coffee and roasting products. Food Funct. 2011 Sep;2(9):529-40. doi: 10.1039/c1fo10055f.
  5. Akimoto K, Inamori M, Iida H, et al. Does postprandial coffee intake enhance gastric emptying?: a crossover study using continuous real time 13C breath test (BreathID system). Hepatogastroenterology. 2009 May-Jun;56(91-92):918-20.

†Results may vary. Information and statements made are for education purposes and are not intended to replace the advice of your doctor. Global Healing Center does not dispense medical advice, prescribe, or diagnose illness. The views and nutritional advice expressed by Global Healing Center are not intended to be a substitute for conventional medical service. If you have a severe medical condition or health concern, see your physician.

  • R Mac

    This was very informative information. I was not aware of the effects of decaffeinated coffee. I’ve tried coffee alternatives like Pero but nothing can take the place of an original cup of joe. Moderation is key.

  • Betsy S

    I personally found a “LOW ACID” coffee produced and sold by a small company in Minnesota. I performed the ph test on this coffee, which came out neutral, as compared to a popular local cafe’s coffee product. The ph test on the popular local coffee was off the chart “ACID”. I believe that if you can find a “low acid” coffee (which I did), you can help curb the negative condition in your gut produced by this acid. I am not sure I can tout a product in this discussion, but will add it if it is allowed.

  • Donna

    this was very informative. I did know though about the acid level in coffee. I personally gave up caffeinated coffee a few years ago and only drink 2 coffee mugs of organic decaffeinated only and that is only after I eat breakfast. I have had stomach problems in the past where if I eat anything acidic on an empty stomach sends it into all kinds of spasms. I have had that under control for many years now. I do really enjoy this news letter.

  • Gina DiResta

    I can NOT believe this was just sent to me!! I have been having largospasams and went off coffee just yesterday and for the 1st night ever I didn’t have one!!!

  • yolie

    Thank you for the information. This will be a challenge. Is there a right way to drink your coffee, even if using moderation.

    I now understand never to have on an empty stomach.
    Plz advise.
    Thanks again

  • Vincent Regan

    I drink 3 cups of coffee a day and have stomach pain for three years every morning about 6 o’clock in the morning goes away After a tums went to the grocery store four days ago and they didn’t have my regular cream so I Got fat free cream pain have gone a way.

  • Nicola Fernandes

    Hi, I was diagnosed with H Pylori as a child and over the years got addicted to drinking coffee and of course always suffering from a
    painful stomach. Have since stopped drinking it everyday for about 10 years and when I do the symptoms start all over again.

  • Nancy S

    Thank you for this information, learned a few new things about coffee drinking. I love coffee and have weighed the benefits vs the potential harm over the years. I have found that making my coffee with 9.5 pH alkaline water significantly reduces the acidity of the coffee and actually improves the flavor (less bitter). I also only drink organic coffee because I believe the chemicals used to grow non-organic coffee are the worst health risk. I also drink it black. Years ago, I gave up coffee because it was upsetting my stomach and then I read something about the combination of coffee and dairy causing stomach issues. So I tried drinking coffee black, learned to like it, and never had stomach issues again. I also try to drink no more than 1 cup a day. Any more than that I believe puts too much stress on the adrenals.

  • Horvath Ernone

    I used liver detox and I felt to be more free

  • John Trefry

    I love my coffee, and have no difficulties with it, gut-wise. And I enjoy all of the proven benefits. I go for around 4 cups a day.

    What I have been doing lately, as a preventative measure is drinking “cold brewed” coffee. Simply put, soaking fresh ground beans overnight (12 hours) to produce a concentrate, filtering it and putting it in the fridge. To use, i just dilute it 2:1 (water to coffee concentrate).

    The “cold brewing” leaves a lot of the harmful acids in the grounds, and creates a much smoother, almost “sweet” flavor. Exceptional as an iced coffee. For hot coffee, I just toss it in the microwave for a few minutes. Google “cold brew coffee recipe”. There are lots of recipes out there, but I use one cup of whole beans, ground coarse (it makes filtering easier – you can grind it fine, but its harder to get the sediment out.), and add 3 cups of water. Overnight on the counter for 12 hours, and time to filter.
    You can also do this with cold water and a French Press for smaller batches.

  • Altamisal

    Because of the reasons listed here as well as the fact that it contributes to weight gain by raising insulin and cortisol levels, I quit coffee a few months ago. Now I’m able to fit in some of my clothes that were too tight before.

  • Barbara Dunn

    This sounds great, I have to try it! I love coffee but I can’t drink it because it “burns” my stomach. Maybe this way I can tolerate it better.

  • Lady Tam Li Hua

    I usually don’t have too much a problem with it, as I only drink a 12 oz mug’s worth a day, if at all. However, I’ve noticed an intense increase in cramping if I drink it right before my monthly is about to begin. (Of course, I never realize this until AFTER the cramping has started.) Any other time, it’s usually fine. Yay for weird bodily functions!

    ADDENDUM: I’ve found that the amount of crampage is GREATLY reduced when I make my own coffee – instant *or* brewed – than when I attempt to drink something someone else made. I don’t know if I just make mine far weaker (I rarely ever use the same amount suggested by the bottle or box, and go for a little less), or if others make theirs far too strong (whether individuals or baristas), but generally I’ve found this to be the case.

  • EastCoastCommentator

    I also read instead of cream a bit of coconut milk, almond milk something your body can handle. sometimes the milk is inflammatory to you stomach and intestines

  • dauden

    Agree with this comment. I also use alkaline water to brew, buy my coffee green and roast at home, but use raw, local organic cream to taste. One to one and 1/2 cups each morning is my dose. My body will tell me I’ve had enough. I enjoy it immensely!

  • DQ202

    What’s the point of drinking decaffeinated coffee? I don’t get it, why not just quit altogether or are you addicted, just curious.

  • DQ202

    What benefits? Only reason to go to all these lengths to drink something that is clearly bad for you is addiction.

  • DQ202

    What do you recommend, Betsy?

  • DoubtingThomas

    Well, not really, but the important thing is that you got to feel cool with that witty line.

  • mnbk

    I agree with you completely — the article you linked is bullshit.

  • Gravest Amigo

    Just stop drinking coffee if it makes your thinking process that slow 🙂 Babbling about your personal food intolerance all over internet is odd.

  • Lisa Brown

    I have never drank coffee and I even stopped drinking anything with caffeine several years ago. However, I do organic coffee enemas several times a week. It has a different effect when used this way. My husband drinks a 12-cup pot every morning. We found him an organic brand that he likes a few months ago. He had an ulcer blow in the mid-90’s but that more than likely was caused by tainted water on the military base in Korea.

  • Russ Jones

    2 cups in the am and I’m rushing to the bathroom

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