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Does Coffee Cause Autoimmune Disease?

coffee and autoimmune disease

The Connection Between Coffee & Autoimmune Disease

83% of adults in the US consume coffee. That number comes pretty close to the estimated 46 plus million people with autoimmune disease. So the big question is – Does coffee cause or contribute to autoimmune disease? Recent research shows that several forms of autoimmune disease are linked to coffee consumption. But the truth of the matter is, it’s not just the coffee. It is how it’s made, how it’s grown, how it’s served, what it is served in, and how much of it you choose to drink. I know…it’s never a simple black and white answer.

Does coffee cause autoimmune disease? Let’s dive into the basics on the topic:


Autoimmune Diseases Linked to Coffee

A recent study found that coffee consumption was linked to rheumatoid arthritis, type I diabetes, Hashimoto’s thyroiditis, and celiac disease. The same study found that coffee contributes to gastro-esophageal reflux disease (GERD – see image below). Other studies have found that coffee can cross react with gluten, and that some instant coffees are actually cross contaminated with gluten. In my practice, it is common to see people with existing autoimmune disease feel worse when they consume coffee. At this point, you are probably getting mad at me for sharing this information, but don’t shoot the messenger, and don’t stop reading. The rest of this post is very revealing.

Coffee causes heartburn

Think About This When You Are Drinking Coffee

It’s not just the coffee. Although research does show that coffee consumption is linked to autoimmune disease, you also have to consider several other factors common to coffee consumption.

What you put in the coffee matters

Many don’t just drink black coffee. They add dairy, non-dairy creamers, nut milks, sugar and artificial sweeteners, and other GMO fillers. Because dairy is often processed with microbial transglutaminase (meat glue), and can mimic gluten, it poses a threat for those struggling to overcome autoimmunity. Non-dairy creamers are full of GMO corn syrup, highly processed oils, and other chemical additives known to trigger autoimmune disease. Nut milks often contain gum thickeners known to cause inflammation to the GI tract. Sugar is definitely a contributing factor in autoimmunity, and now research is linking artificial sweeteners to autoimmune thyroid disease.

Quantity Matters

Many people are habitual coffee gulpers, taking in as much as a pot of coffee per day. It is important to understand that too much coffee comes with too much caffeine. Caffeine is a nervous system stimulant that disrupts a healthy sleep cycle. Sleep disruption is one of the primary triggers in autoimmune disease. High doses of caffeine also acts as a diuretic, contributing to the loss of minerals, water soluble vitamins, and dehydration. High doses of caffeine can also trigger excessive cortisol release from your adrenal glands, leading to large fluctuations in blood sugar, weight gain, and muscle loss. All triggers in the autoimmune process. So for some, it is not the coffee per say, but it is the quantity consumed on a regular basis.

The Cup Matters

What you put your coffee in is also important. The throw away paper cups used by most coffee bars and restaurants are lined with a coating often created from polylactic acid derived from GMO corn or sugar sources. Some linings are made from polyethylene derived from petroleum. And don’t forget, the lids and stir sticks are derived from plastics containing endocrine disrupting chemicals like BPA that have also been linked to autoimmune disease.

Who Should Avoid Coffee?

If you have a diagnosis of autoimmune thyroid disease, celiac, rheumatoid arthritis, type I diabetes, GERD, peptic ulcer disease, or Barrett’s Esophagitis, avoiding coffee is probably a good idea for you. If you have a leaky gut, avoiding coffee is probably a good idea, at least until you resolve the issue. Don’t forget that some people are also allergic to coffee. So if you aren’t sure, ask a functional medicine doctor to test you for this. And most importantly, pay attention to how you feel. If drinking coffee causes you problems, stop drinking it. In my practice, coffee is most commonly linked to autoimmune joint pain, muscle pain, anxiety, sleep problems, and gut irritation. So start with looking for those symptoms first.

Coffee Substitutes

If you find that coffee creates problems for you, try using green teas, herbal teas, bone broth, or a

If You Must Drink Coffee

If you will not give coffee up, consider the information above as a guide. Keep your consumption reasonable (1 cup/day). Consider the source of the coffee. Organic, whole bean is best in order to avoid mass pesticide exposure. Avoid using pod based machines. The water tanks in these commonly grow mold which can also be a trigger for autoimmune disease. If you use an instant coffee, make sure that it does not contain gluten. Drink out of a real glass and avoid the plastic based toxins. Drink your coffee in the morning to minimize the effect it can have on your sleep. Avoid drinking your coffee with chemical additives.

Two brands that I can highly recommend are:

  1. Purity Coffee – This company is a whole bean, certified organic, mold free coffee.
  2. Organo King Coffee – This instant coffee is organic, gluten free, and contains reishi spores. I like it because reishi has immune modulating effects that have been show to be supportive for those with autoimmune disease.

Alright, now that I have turned you into my enemy;) leave your scathing commentary below! Or you could just share your experience with coffee and autoimmune disease.

Always looking out for you,

Dr. Osborne – The Gluten Free Warrior

56 Responses

  1. Dr Perlmutter says 1 8 oz cup of “black coffee” contains 1,000mg of magnesium. Also NRF2 a pathway for anti oxidant & detox.

    Organic, whole bean, plus no tap water.

    Yes. I’m a coffe lover. I also do another cup with coco oil & butter

      1. For those who need caffeine, is substituting other caffeine supplements – gums, caffeine tablets- an ok option? Is it the caffeine which interacts with immune system or the other compounds in coffee? I am a shift worker and no coffee would make my job very difficult

  2. Our culture doesn’t stop at just one normal cup of coffee. It has to be large, fancy named coffee with tons of sweeteners in it.
    I lived in Italy for several years, and the local coffee bars would roast their own beans. At the bar on my street, the staff knew everybody’s name, and how they liked their coffee. There was never a to go cup, but rather a proper cup and saucer, and a modest amount-nothing supersized. Very little milk in fact. Along with the coffee, were fresh juices offered, with carrots, oranges, lemons and green apples. I miss that, but what I miss the most are the connections with everyone at the bar every morning.

    1. You are awesome, Dr. Osborne.
      I look forward to every bit of your accurate information and objective presentation.

    2. I totally agree! When you do it right, there’s great benefit. Add a bit of class, and conversation, and the coffee ritual turns into a healthy life giving point of connection. The Italians got that right…

  3. I enjoy my one cup of organic coffee with coconut milk and MCT oil each morning but I will gladly give it up if it will be beneficial for my health. I have auto immune disease and thyroid issues and a yeast overgrowth that I cannot get rid of…. I am willing to do anything… I trust you!

      1. Do they have a caffeine free coffee? I did away with caffeine, causes inflamation for me but decaf coffee is ok.

        1. Teecino offers caffeine free coffees made with chicory root or dandelion. Delicious and delightful! I have problems with the caffeine too which I believe to be more of the issue with coffee and immune disorder correlations.

      2. Are you saying yes, you can drink this while you have a suspected autoimmune issue or not until you have cleared up the issue.

  4. Very good article.. well said.
    The experts’ points of view are sharp, critical,deep thought, experienced.

    Well said n thourough info. Thank you for sharing

  5. Your discussion of America’s preferred morning drink and it’s most likely effects on my arthritis is blatantly lacking as it does not address a possible alternative. No mention of any type of tea as a substitute. You cannot just conclude that coffee is bad for folks like me without mentioning an alternative-plain & simple! Poorly fleshed out article that leaves me with little info and plenty of questions.

    1. Hi Jim,
      I know this article would come with criticism. I did not condemn coffee in this article. I informed of the potential problems. Sorry that wasn’t helpful for you. As for alternatives
      1. Organic Tea – black, green, herbal…
      2. Hot water with lemon
      3. Bone broth
      All the best,
      Dr. O

      1. I’ve occasionally used dandelion (Dandy Blend) as a yummy coffee substitute! Have celiac, Hashimotos, and RA. Feel so much better when I’m not drinking coffee 🙂

  6. Thanks for the info! I now drink 2 cups cold brew organic with no sugar just organic coconut milk! Love cold brew on ice so much have to make myself stop at 2 only before noon otherwise it does affect my sleep! Awesome info always!!! Thank you very much

  7. What about organic, Swiss water process decaf coffee freshly ground from whole beans? That is what I drink 3 – 4 cups a week with coconut milk.

  8. My coffee consumption has Been dramatically increased over the last several years, but most recently things in my health- I wake up in the evening with my hands swollen and hurting and then as the day gets on its much better. A couple of years ago I started having problems with my hips ( bursitis & osteoporosis) now I can barely walk after sitting in the car and driving for two or three hours I feel like I’m 85 years old and it is very discouraging- I wasn’t putting it together till now

  9. I have one cup a day half decaf organic coffee, half chicory, a little organic milk and coconut sugar,half tspn. Coffee is acid,so the chicory balances. I do have autoimmune disease though, and yeast overgrowth.I only got very ill after putting on weight, but have had colitis far longer. I’m confused and suffering not knowing a real cure yet. I think now though an alkalising diet and no sugar is the answer. Acidic system causes so much illness I now read. So much rubbish food is acidic.Keep a diary of how you feel after certain foods. Grumpy and lumpy, or light and happy. Your body knows.

    1. I switched to the Organo King coffee and have been loving it. I only drank decaf for the last 10 years but have been reading how that isn’t great for you. I switched upon a recommendation from my Functional Medicine doctor that the Reishi was very good for my Hashimoto’s. It has lowered my free cortisol way down to norms again after 3 months of having 2-3 sachets of coffee a day. I love my coffee and am really happy to have found an alkaline form of coffee that is truest healthy for me.

  10. As someone who is suffering from hashimoto thyroidits I had no idea that coffee was a hugh problem! I am so grateful to know this as I drink a lot of coffee everyday! So immediately …..I am no longer drinking it. And excited to see how I feel in a month! I have been feeling really bad lately… desperate to try anything. Thank you for all you do for us and God bless you for this article. Will let you know how I am doing.

  11. So here I was sitting down for a quiet moment…with a coffee! Organic of course, no sweeteners. As I wondered this morning why on earth I was stiffer than usual and what I could possibly do, I realised coffee may be on the list to go. And now I read this. It’s a tough call. I know somebody else commented they may need hypnotherapy and I’m kinda thinking maybe we could get a group discount! I hear you Dr Osborne…now to take the step. Man I love my coffee in the morning – the taste and the kick it gives. This is hardcore!! But worth it.

      1. Ok, so I’m late to this, but isn’t the king coffee from Organo still coffee with caffeine? But with reishi mushrooms? I guess I’m wondering how it’s ok for autoimmune folks. I know coffee makes me feel terrible physically (more pain, anxiety later, gut pain, poor sleep), but I crave it for the neurotransmitter high. I’m taking Zonegran and it causes depression.

  12. Intetesting article and perhaps coffee was a trigger for my autoimmune as I was drinking a lot of coffee before diagnosed with Scleroderma; I have stayed off since because of caffeine affecting Raynaud’s . I bought some bags of organic roasted chichory as heard it tastes like coffee but I don’t realky think so. I heard chicory was good for your gut because of its inulin. Then I heard somewhere else that you might want to limit the amount because the inulin could also feed bad bacteria not just the good but I am not sure if this is true or not – do you know about this Dr. Osborne? Thank you kindly!

      1. Thanks for your reply Dr. Osborne. This makes me a little afraid to drink roasted Chicory now too then if an irritant to the mucosal lining. Do you think 1 cup a day be ok or should be avoided if you have Autoimmune?

  13. Dr.O; listened for yrs. I wasn’t ready to quit becuz I love cheese & blue corn chips (also ate rice flour in baked products) Abt 2 wks ago, ran my own “allergy test” with dairy. One day ate all cheese I could: a lg bowl (8+ oz) cot. cheese = Bkfast; Lunch =pizza slathered w cheese; & Dinner lg slice (3+ oz) Colby-jack. Yeppers- AI flare didn’t wait til morning; began abt 11 pm when I was getting ready to go to sleep-the most painful flare I’ve had in years. Miss the cheese but not the dime size phlegm I used to have stuck in my throat. Last week, I ate some corn chips with chili & in 20 min started itching on extremities & belly. Haven’t tried to eat rice with a meal-don’t like rice enough to test it. AI=RA, Hashimoto’s, Fibromyalgia, -also osteoarthritis, MDD recurrent but no depressive episodes in abt 10 yrs, 2 heart attacks 7-2018 & then 2 stents placed in coronary arteries. Cardio doc unhappy I’m not taking his meds. Re-evaluating supplements -adding back Vit D, omega 3, digestive enzymes, probiotics. Pain level increases after taking, guessing some gluten or dairy in there somewhere. Also love cola and root beer-those will be the hardest to quite (albeit probably most helpful) & stop poisoning my body.

  14. I have recently switched to chicory in stead of coffee. I’ve also cut out all grains, legumes, dairy, nightshade, nuts, and sugar. I have had RA for decades and recently diagnosed with Hashimotos. What are your thoughts on chicory for autoimmune disease?

      1. Chicory can be very acidifying if one has a lot of it. It is also often “cut” and roasted with wheat, i.e. gluten.

  15. So great you also mention the to go cups Dr. Osborne!!!!! Before going completely organic with coffee, I did have the occasional stop at Starbucks and instantly upon sipping from those toxic cups, my tongue would burn and feel burnt for hours. Once I learned what all can make up that lining, I only use my own tumbler wherever I go. Thank you for mentioning that dirty aspect. And you get only praise and gratitude from me that you’ve covered so much about coffee, the good and the bad. Helps to make so much sense of reactions!

  16. I have found the videos on gluten and on coffee very informative. I have an allergy of some kind; definitely dusts, and, intend on getting the genetic test. My daughter had JRA was treated for it and now has diabetes. So,I am interested in knowing if i have GI if i may have genetically transmitted something to her.

    p.s. ( I find the videos very informative but I find the cursor sometimes / oftentimes difficult to follow on the “small” screen (laptop). When doing presentations for video would you mind increasing the size of the cursor and perhaps adding a color such as high red, high yellow, or, light blue to it to make it easier to follow ( when your presentations get a bit fast paced)…thank you.

  17. Didn’t think I could do it but I eliminated coffee from my diet a little over 2 months ago. Tried to reintroduce it about 2 weeks ago. Turns out it gave me a similar reaction to gluten AND I don’t even like it anymore. Sadly, I still like chocolate but it does the same thing as coffee.

  18. Thankyou for the information, I suffer from sjogrens syndrome and chemical gastritis, and Hyplori I drink a lot of coffee but today I bought organic coffee and organic coconut sugar

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