How bad is coffee really for our gut health? Do we really need to give it up? We’ll look at exactly how coffee contributes to leaky gut, plus how to decide when to quit (and when to try it again).
Last Updated: Dec 17, 2022
In this guide, you’ll discover…
Well, as an avid coffee lover, neither of us are going to like what I’m about to write…
…you see, coffee is how I used to start every glorious day. Notice that past tense? Yeah, unfortunately I’m a recovering coffeeholic.
Instead of drinking a rich creamy cup of coffee every morning, I tend to sip on some lightly brewed Yerba mate these days, along with gut-nourishing L-Glutamine water (using this L-Glutamine powder).
It might not sound like the stuff of dreams, but guess what?
My gut is in amazing health. No more stomach pains, no heartburn and little to no chronic systemic intestinal inflammation. The knock on, and ironic, effect is that my energy is supercharged compared to the days when I drank coffee.
Best of all, Yerba mate in particular delivers a much steadier buzz and type of clarity than coffee ever did. I’m happy!
P.S. for all my ideas on saying goodbye to leaky gut, download my FREE leaky gut ebook here.
Starting the morning with coffee was the most natural habit in the world. It was also a great trigger for turning my brain on and getting focused.
I would pour my coffee and almost instantly start work. Within 20 minutes I’d have knocked out all my emails and be on the way to ticking off my first task for the day.
Better yet, I used to make a ‘Bulletproof’ style cup of coffee every morning. This involved brewing high quality beans (touted as being mold free), then blending it with grass fed butter, coconut oil and chocolate protein powder.
It produced the frothiest, tastiest coffee you could imagine. I jumped out of bed every morning for it!
So when it came time for me to drop my pimped up cup o’ joe, it was tough.
That’s why I get it if you’ve reached this article after first debating for hours whether to kick the habit and then Googling around for things like “does coffee really cause leaky gut”.
In fact, you might be thinking…
There are countless studies pointing to the benefits of coffee. From lowering people’s chances of cancer, stroke and diabetes, to even helping to ward off the risk of Parkinson’s1.
Plus the antioxidants and polyphenols found in coffee work wonders2 – leaving many studies to conclude that coffee helps extend your longevity, outright.
But here’s the thing about coffee…
…you can get those benefits from drinking Yerba mate3 or green tea4, or better yet, green shakes (think kale, broccoli, avocado, cucumber etc!).
More importantly, coffee is actually bad for you if your gut is in poor health. In other words, the net health result for people with leaky gut is negative.
I’ll explain why in a minute.
But before you get too depressed you should know that it is possible to pick coffee back up again in a few months when you heal your leaky gut. There is hope!
For example, every now and then when I have a big deadline I might brew one of my butter, coconut oil, protein powder super coffees. And I will love it and wonder why I ever turned my back on my preciooous.
You see, now that my gut is healed it can handle the occasional cup o’ Joe. Perhaps what I like most about this occasional use is that it feels like a real treat and the benefits of the caffeine surge are immense.
1) Coffee is like wheat, kinda
If you’ve done even a cup of coffee’s worth of reading about leaky gut, you’ll know that wheat, and grains in general, are our gut’s enemy. That’s due to the fact that they are seeds, and in order to survive, they are designed to avoid being digested – and instead be pooped out intact so they can replant and reproduce. Well, coffee, like wheat, is also a seed as it’s made from the pit of the coffee fruit.
That said coffee is not as strong a fighter / anti-nutrient as something like wheat. But still, it’s bad enough for those of us suffering with a leaky gut to avoid to avoid since it also affects our gut bacteria, which could contribute to leaky gut5.
2) Coffee is like gluten, at least that’s what our bodies might think
If you have gluten sensitivity, then you should approach coffee with the kind of caution you would a big steaming bowl of pasta. You see, it turns out coffee is one of the most common cross-reactive foods with gluten6. In other words, the body can mistaken coffee proteins for gluten.
And that means, just like it would produce antibodies to attack gluten (thereby causing inflammation) it might do the same with coffee.
Although I am not very far down the gluten sensitivity scale, it’s enough of a risk to say goodbye to coffee for the sake of your gut health.
3) Heartburn, oh glorious heartburn
One cup of coffee was never enough to give me heartburn. It was only on the long work days when one cup quickly became three or four, that I felt heartburn come racing up. It makes sense too given that coffee, including the innocent looking decaf, can cause excessive secretion of gastric acid7 and speed up gastric peristalsis, or movement of the intestines8.
4) Us autoimmune (AI) folks, and anyone suffering from adrenal fatigue, in general, don’t play well with coffee / high caffeine intake
Coffee has been shown to increase the risk for AI illnesses, such as rheumatoid arthritis9. Therefore, I think it is best to abstain from coffee if you have AI issues. After all, AI issues can stress our bodies out significantly, pushing us towards adrenal fatigue, and when you add coffee on top of that things can just get worse.
In order to help your leaky gut repair itself, I recommend first giving up coffee completely for 30 days. Then on day 31 you can try coffee again and see how your substantially-improved gut responds to it.
When I first realized I would have to eliminate coffee I imagined it would be like a scene out of Trainspotting. Goodbye coffee, hello Glasgow pub restroom!
And that is why I spent hours working out the perfect way to wean myself off coffee without experiencing withdrawal, in both physical and psychological senses.
Here’s the plan I used to easily quit coffee
- Switch to green or black tea – something with caffeine – for the first 7 days. It contains just enough caffeine to make life bearable. You won’t crash and burn at work, and you’ll enjoy the steady buzz these teas give compared to the highs and lows of coffee.
- Alternatively, supplement with caffeine tablets during these 7 days. Start with 100mg caffeine and taper off throughout the week. If going this route, I recommend taking a caffeine + L-theanine10 (green tea extract) supplement. The L-theanine works very effectively to smooth out the energy of caffeine, so you never experience the feeling of a crash after your energy boost11.
- During this first week, feel free to drink 1 cup of decaf coffee a day if you really miss the smell and taste of coffee. But understand that, when it comes to leaky gut, decaf is just as bad as normal coffee for leaky gut. I would recommend a quality decaf like Swiss Water but to be honest there’s really no point buying it, given you’re only going to indulge in decaf for one week.
- Now it’s week 2. This is the time to really give your gut a rest. That means no caffeine (so no green/black teas) or decaf coffee. Although eventually, once you’ve improved your health, you can enjoy these, right now we want to heal your gut fast. At this point I recommend you switch up to caffeine-free herbal teas, especially those that are good for digestion, like ginger. Where possible make these teas yourself, eg instead of an actual ginger teabag or leaves, simply slice up some fresh ginger and add to hot water with a squeeze of lemon. (I remember this simple drink slotted in perfectly into my morning routine. It’s also a heck of a lot more enjoyable than starting the morning off with a steaming cup of bone broth – one alternative to coffee I’m just not game for in the AM).
- Stay the course. Seriously. It’s only 3 weeks of no coffee and no caffeine. Think of this as a personal challenge – and boy, your gut will definitely feel the personal benefits. Keep your eye on the prize here and be sure to stick it out for the full duration!
I think you’ll find it so much easier to reduce or completely eliminate coffee, if you have a list of all of the healthy alternatives that can partake in your morning routine without the side of leaky gut.
The type of drinks your gut will loooooove!
So I spent a week working with my research team to judge pretty much every mainstream beverage idea against gut health criteria (specifically leaky gut). We filtered them down one by one and we ended up finding the top 16!
But not content on stopping there, we decided to do the painstaking work and rank them from best to not-quite-as-good. And wow, did we have a few heated discussions amongst the team.
The end result is of course worth it and you can view our leaky gut Drinks Pyramid here.
Print it off, keep it around and you’ll never run out of cool ideas for coffee alternatives!
After your month without, you can reintroduce coffee and see how you react. But that’s only if you now feel in good health and haven’t had any issues over the last 4 weeks. Ie if you are feeling significantly better and can consider your gut mostly healed.
When I went off coffee I was still not completely healthy within 30 days – most people with an autoimmune condition, adrenal fatigue, IBS, IBD, celiac etc, will probably be in the same boat. Whereas other people who had milder problems or were reacting to coffee in the same way as gluten may notice an almost miraculously quick improvement!
In my case, the former was the case, so I waited roughly 3 months to try coffee again. And then I found it sat fine with me, as my gut was much happier and healthier by this time.
But I realized it wasn’t a habit I wanted to get back into for fear it would inflame my intestines again, however minor, and tip my gut back over to the leaky side.
Also, interestingly I discovered my taste for coffee had dissipated significantly. I still loved the smell – wandering into a coffee shop will generally send me off into la la land. But overall, my taste buds had adjusted away from the taste and it didn’t have the allure it once did.
At this 3 month mark I also added Yerba mate tea back into my life. This I kept. It is my new morning routine and a wonderful provider of smooth and light energy without the crash that typically comes along with coffee. It gives a certain clarity and focus to my work that coffee rarely did.
Of course I do dip into the coffee jar now and then. In the last month I’ve had one ‘Bulletproof’ style coffee and it was great. But that’s just about my monthly quota. And this setup works perfectly. It may take some adjustment, but over time I bet it will for you, too.
P.S. if you want to get your gut back to health so you can also drink the occasional coffee then I recommend you checkout my FREE leaky gut ebook here. (PDF download)
- Butt MS, Sultan MT. Coffee and its consumption: benefits and risks. Critical reviews in food science and nutrition. 2011 Mar 25;51(4):363-73.
- Yamagata K. Do coffee polyphenols have a preventive action on metabolic syndrome associated endothelial dysfunctions? An assessment of the current evidence. Antioxidants. 2018 Feb;7(2):26.
- Gan RY, Zhang D, Wang M, Corke H. Health benefits of bioactive compounds from the genus Ilex, a source of traditional caffeinated beverages. Nutrients. 2018 Nov;10(11):1682.
- Suzuki Y, Miyoshi N, Isemura M. Health-promoting effects of green tea. Proceedings of the Japan Academy, Series B. 2012 Mar 9;88(3):88-101.
- Nishitsuji K, Watanabe S, Xiao J, Nagatomo R, Ogawa H, Tsunematsu T, Umemoto H, Morimoto Y, Akatsu H, Inoue K, Tsuneyama K. Effect of coffee or coffee components on gut microbiome and short-chain fatty acids in a mouse model of metabolic syndrome. Scientific reports. 2018 Nov 1;8(1):1-0.
- Vojdani A, Tarash I. Cross-reaction between gliadin and different food and tissue antigens.
- Rubach M, Lang R, Seebach E, Somoza MM, Hofmann T, Somoza V. Multi‐parametric approach to identify coffee components that regulate mechanisms of gastric acid secretion. Molecular nutrition & food research. 2012 Feb;56(2):325-35.
- Piric M, Pasic F, Rifatbegovic Z, Konjic F. The effects of drinking coffee while recovering from colon and rectal resection surgery. Medical Archives. 2015 Dec;69(6):357.
- Sharif K, Watad A, Bragazzi NL, Adawi M, Amital H, Shoenfeld Y. Coffee and autoimmunity: More than a mere hot beverage!. Autoimmunity reviews. 2017 Jul 1;16(7):712-21.
- Cho HS, Kim S, Lee SY, Park JA, Kim SJ, Chun HS. Protective effect of the green tea component, L-theanine on environmental toxins-induced neuronal cell death. Neurotoxicology. 2008 Jul 1;29(4):656-62.
- Cichello SA, Begg D, Weisinger R. Anxiety behaviour displayed in C57BL/6J mice consuming coffee and cocoa, but not observed in mice consuming Japanese green tea in a high fat diet induced obesity model. Current Research in Nutrition and Food Science Journal. 2014 Apr 28;2(1):33-9.