The Pros and Cons of Coffee

July 5, 2012 in Categories: , , by

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Coffee drinkers around the world cheered when research study after research study proved that drinking coffee in moderation could provide a range of health benefits; including: preventing cancers, preventing stroke, preventing diabetes, preventing cardiovascular disease, preventing depression, preventing antibiotic-resistant bacterial infections, preventing cirrhosis of the liver, preventing gout, preventing gallstones, and preventing Parkinson’s and Alzheimer’s disease.  It can even reduce muscle soreness after a workout!  There are studies that show that you are plain old less likely to die (from any cause) if you are a coffee drinker! 1  This implies that drinking coffee every day can actually extend your life!  (This Wikipedia page has links to some of the many science articles showing coffee is beneficial).  In the paleo community, these health benefits are often cited to rationalize our addictions (coffee contains mild psychotropics) to this delightful beverage (what I generally think of as “comfort in a cup”).  Let us all raise our mugs of hot delicious americanos (whipped with coconut oil) in toast!

Er, not so fast.  Coffee is made from a seed (not a legume, but the pit of the coffee fruit).  Right away this should put us on the alert since seeds tend to contain protective compounds to prevent digestion and thereby ensure the survival of the plant species.  In the case of wheat, those compounds cause increased intestinal permeability (i.e., leaky gut) and prime the immune system to exaggerate inflammation and potentially cause autoantibody formation, which is clearly detrimental to our health.  In the case of the itty bitty seeds in blueberries, those compounds have such a low toxicity level as to have a negligible effect on our health (and the beneficial antioxidants and polyphenols in blueberries more than compensate!).  So, where on that spectrum is the coffee bean? 

Coffee is very rich in antioxidants and polyphenols.  Many of the health benefits of coffee are attributed to these substances.  These chemicals are also found abundantly in fruits and vegetables, which is why a diet rich in plant matter has pretty much the same list of health benefits as coffee (well, actually, far more health benefits).  Some of the health benefits of coffee are directly attributable to its caffeine content (which is also why drinking tea which is rich in antioxidants, polyphenols and also contains caffeine is also associated with good health).  This is partly why many of the beneficial effects of coffee are not seen with decaf coffee.  Also, the decaffeination process tends to strip the coffee not only of much of its caffeine content but also many of its antioxidants and polyphenols (potentially leaving behind a few of the more harmful substances that can be found in coffee). 

A large percentage of people report that coffee upsets their stomach or gives them heartburn.  This is because coffee stimulates the secretion of the main gastric hormone gastrin 2.  This causes excessive secretion of gastric acid and speeds up gastric peristalsis (even decaf coffee has this effect).  Coffee also stimulates release of the hormone cholecystokinin (CKK), which stimulates release of bile from the gallbladder.  In a healthy individual, this release of bile salts is likely sufficient to neutralize the highly acidic chyme.  However, deficiencies in gall bladder function are associated with metabolic syndrome 3.  In the case of reduced gall bladder function or excessive coffee consumption, highly acidic chyme travels through the small intestine where it irritates and inflames the lining of the intestines.  This is also clearly a good argument for consuming coffee with food.

One of the detrimental effects of consuming caffeine (whether from coffee, tea, chocolate or energy drinks) is the effect that it has on cortisol.  Caffeine acts to increase cortisol secretion by elevating production of adrenocorticotropic hormone by the pituitary gland 4.  Excessive cortisol production can lead to a variety of health issues, including an overactive immune system, disrupted sleep, impaired digestion, and depression.  When you consume caffeine, your cortisol level increases (dependent on what your cortisol management is like to begin with and how much caffeine you consume) and can stay elevated for up to 6 hours.  With daily consumption, your body will adapt somewhat and not produce quite as much cortisol, but complete tolerance to caffeine does not occur 5.  Very importantly, if you are a habitual consumer of caffeine, your cortisol will increase more dramatically in response to stress (like that guy cutting you off in traffic) than someone who doesn’t consume caffeine 6,7.  If you have difficult managing stress as it is, caffeine is not helpful to you. 

One key study showed that moderate coffee consumption in healthyindividuals correlated with increased markers of inflammation in their blood 8.  People who drank more than 200mL (that’s one large cup in my house) of coffee every day (equivalent to 37.3mg of caffeine) had increased circulating white blood cells and several key inflammatory cytokines (chemical messengers of inflammation, usually restricted to the site of injury or infection).  When cytokines circulate in the blood, they cause low level inflammation everywhere in the body.  This chronic systemic inflammation is exactly one of the situations we are trying to prevent with adoption of a paleo diet!  These increases in markers of inflammation were persistent even after adjusting for other health and lifestyle factors (such as age, sex, weight, exercise, and smoking).

If you have celiac disease or gluten sensitivity, extra caution should be used when consuming coffee.  Internal data from Cyrex Labs shows that for people who produce IgG or IgA antibodies against gluten (i.e., gluten sensitivity), coffee is the most common cross-reactive food.  This is because there is a high degree of homology between some coffee proteins and gluten (this means the proteins look very similar so if your body is producing antibodies against gluten, they are more likely to also recognize coffee proteins).  Food sensitivities are one of the main issues that prevents the body from fully healing after adopting a paleo diet.  If your health isn’t improving as dramatically as you expected after adopting a paleo diet and if you are gluten-sensitive, continuing to consume coffee may be the culprit. 

So, should you drink coffee or not?  Are you tired of hearing me say “it depends”?  It does depend.  If you are very healthy, have lost most of the weight you need to lose, have regulated your hormones and healed your gut, coffee (in moderation) is likely to provide you a health benefit (Yay!).  This benefit is likely comparable to drinking tea and/or consuming diet rich in vegetable matter (I’m trying to say that if you don’t like coffee, don’t go out of your way to drink it).  However, in people just starting their paleo journey, especially people with evidence of metabolic derangement, giving up coffee for at least a little while will likely speed up the healing process (D’Oh!).  Also, caffeine in general is contraindicated for those with adrenal fatigue. Those people with autoimmune diseases should take special care with consumption of coffee as their systems are particular sensitive to irritants and they have a much higher likelihood of an immune response to coffee (because they have a much higher likelihood of gluten intolerance and food sensitivities in general).  Overall, coffee gets the “proceed with caution” label. 

 1 Freedman ND. “Association of Coffee Drinking with Total and Cause-Specific Mortality”. New England Journal of Medicine. Retrieved 17 May 2012.
2 Boekema, PJ.; et al “Coffee and Gastrointestinal Function: Facts and Fiction: A Review”. Scandinavian Journal of Gastroenterology 1999. 34 (230): 35–39.
3 Ata N, et al. “The metabolic syndrome is associated with complicated gallstone disease. Can J Gastroenterol”. 2011 May; 25(5): 274–276.
4 Lovallo WR et al. “Stress-like adrenocorticotropin responses to caffeine in young healthy men” Pharmacol Biochem Behav 1996;55:365–9.
5 Lovallo, W. et. a. “Caffeine Stimulation of Cortisol Secretion Across the Waking Hours in Relation to Caffeine Intake Levels”. Psychosomatic Medicine. 2005. 67:734-739
6 Lane, J.D et. Al. “Caffeine effects on cardiovascular and neuroendocrine responses to acute psychosocial stress and their relationship to level of habitual caffeine consumption. Psychosomatic Medicine”. 1990. 52(3):320-36.
7 Lane JD et al. “Caffeine affects cardiovascular and neuroendocrine activation at work and home”. Psychosom Med. 2002 Jul-Aug;64(4):595-603.
8 Zampelas A et al. “Associations between coffee consumption and inflammatory markers in healthy persons: the ATTICA study”. Am J Clin Nutr. 2004 Oct;80(4):862-7.


Thanks for this, Sarah. Helpful! Good thing for me when I am following a paleo diet I don’t crave coffee. It’s probably a combination of feeling healthier in general and sleep being my challenge, but good to know moderation is important so I don’t slip back into my old ways. :-)

Hi Paleo Mom, I have a quick question regarding coffee. I have Crohn’s Disease and Celiacs Disease. I recently within the last 8 months, started experimenting with bulletproof coffee. I can’t tolerate lactose or casein and up here in Canada, grass-fed certified lactose and casein free ghee is nearly impossible to find. That being said, some skin things have started to flare up for me, eczema like rashes on my face. After reading this, I am definitely going to put the bulletproof coffee aside (although I absolutely love it) and work towards fixing my again leaky gut. Did you retest coffee prior to just stopping it for two years? Or did you re-test? I have had blood food intolerance testing 4 years ago, coffee and chocolate came back fine, so I am hoping this is only brief. Thanks, hope to hear from you soon,



how about cold press coffee (that has significantly lower acidity levels due to the brewing process)? does it make any difference?

It’s interesting to me about this, as I gave up coffee 20 years ago because even decaf upset my stomach horribly.

I recently started drinking cold brew, which I make myself made from locally roasted organic truly fair trade beans that I grind, and it actually stabilized my bowels to a degree that hasn’t happened in years (I usually suffer from alternating IBS). Though standard coffee with conventional cream in it would leave me curled up on the floor in gut pain, the cold brew with grass fed raw milk actually seems to help quite a lot. I’m just starting on the paleo journey, and while I think I can deal with giving up the raw milk, I’m leery of starting in on a heavy load of vegetables (one thing that has in the past given me huge digestive issues) without the coffee on board… Thoughts? It’s one of the few things that has actually helped….

> I’m leery of starting in on a heavy load of vegetables (one thing that has in the past given me huge digestive issues) without the coffee on board… Thoughts?

Try organic vegetables (which aren’t covered in pesticides). Or to know what to steer clear of, check out:

I’m not really a coffee drinker, though I have drunk it in the past. I’ve read quite a bit about it since the messages about it seem so mixed. And one thing I’ve come across is the possibility, at least with most blends, of mold contamination, and I’m wondering if that’s more of an issue with those who are ill (which I AM) than those who are not. Supposedly the central American, high altitude, organic wet processed coffee has far less risk of mold contamination. I wonder if the studies made any kind of distinction in the type of coffee used, OTHER than whether it was regular or decaf.

Hi! I suffered from IBS D while in high school due to stress, but it went away when I finished school. My stomach was then fine. I worked an evening shift job, but drank coffee almost everyday and it gave me D within 15 minutes. I figured it wasn’t a big deal, but when I stopped (a good while later), my stomach was messed up everyday, and still is. I used to be able to drink beer, eat dairy and chocolate and pretty much anything without it bothering me. Now it does… Could it be leaky gut or what? What can I do to fix it? I hate living with diarrhea and urgency every morning. Thanks for any help!

I have been paleo since March of ’14 and through a long story..I gave up coffee for a month. Not by choice. My migraines were less often. I happened to have a family member give me a gift card to starbucks and found the next day I could not just jump up out of bed in the morning. I’ve tried several reintroductions between decaf, not decaf… No matter what I do, decaf gives me headaches and in general, decaf or not, zaps every last ounce of my energy. I have never experienced that caffeine high that people talk about. I wonder why my body reacts this way? Any advice? Clues? I’m just about a week off my last try and my energy is slowly coming back day by day, but I feel I am still not 100% lately. Even being paleo so long, I find that I haven’t found that fountain of energy. But, it’s definitely much improved without coffee.Ironic really.

Please tell me where you get grass fed RAW milk??? I live in Las Vegas and we have really weird laws, it is actually a crime to sell raw milk, and if they catch you transporting it across state lines, it becomes FEDERAL! Anyway, there is a guy working on that, but so far the only change is in northern NV. Just wondering, you can message me on FaceBook, or email me

I think the cross reactive in coffee was from contaminated coffee beans. I think it was Dr Kharrizhan that mentioned it in an interview with Sean Croxton…if you buy beans from an exclusively coffee place the contamination doesn’t show up…….the contaminates beans were from places that might have wheat in a vat one week; corn the next; wheat the next; coffee that next….. etc.

Another outstanding and well balanced perspective on coffee. I can attest to this one – after 35 days solid on a ketogenic aip diet with no symptoms and making the most money I ever made in one month in my life.

I had an emotional trigger and what did I do – reach for coffee after 35 days of only having one cup of yerba mate in the morning with maca and coconut oil to start my day doing better than ever. And down the rabbit hole I went. Of course the emotional trigger was based on trauma that is a whole nother story out of the context here.

But in a nutshell I had a woman I have the hots for swoon over me and give me her number and then I got scared because the attraction was like what you see in the movies (thought I had staryed into a dream) and then something in me started running flashbacks of my alcoholic mother telling me nasty things that had me looping out in fear and low self esteem.

[…] Sarah Ballantyne, my go-to girl on all things autoimmune related, is in agreement with Chris Kresser with regard to individual differences in our ability to deal with coffee. She says, “Those people with autoimmune diseases should take special care with consumption of coffee as their systems are particularly sensitive to irritants and they have a much higher likelihood of an immune response to coffee (because they have a much higher likelihood of gluten intolerance and food sensitivities in general). Overall, coffee gets the “proceed with caution” label.” […]

Thank you for the info! I am curious why drinking coffee hinders you to lose weight. Is it because of the inflammation in your body? Could you assume that inflammation doesn’t allow for proper weight lose?

Thanks so much Paleo Mom

Kristel Klessinger

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