Coffee & Autoimmune Disease

Coffee's Impact on Autoimmune Disease

On the autoimmune protocol (AIP) coffee is an elimination.⁣⁣ Contrary to popular belief, this is NOT because of the caffeine content, it is because coffee is technically a seed.⁣⁣ Seeds are eliminated on the autoimmune protoocl because of their phytic acid & digestive enzyme inhibitor, both of which can contribute to the development of dysbiosis and a leaky gut.

I do believe it is also beneficial for many people with autoimmune disease to go without the high levels of caffeine as well, since many of us are experiencing adrenal dysfunction. Caffeine elevates cortisol levels, which are irregular in adrenal dysfunction already, making stress levels and energy levels unpredictable or completely burning you out.

⁣⁣HOWEVER, coffee does not necessarily need to be eliminated for life!

In fact, coffee can be beneficial for some autoimmune diseases, providing anti-inflammatory effects. Coffee also offers a whack of polyphenols that can help to establish a healthy microbiome. Unfortunately, there are still some for which coffee is inflammatory.

Everyone is different. That's why we do an individual elimination and reintroduction and don't just cut all of these things forever!

My Experience with Coffee & Autoimmune Disease

I have gone through many phases with coffee. Post-celiac disease diagnosis, when I had no idea that coffee could in any way affect my autoimmune disorder, I was a total coffee fiend! I was in my early university days when it seemed like coffee was the only thing that could possibly be keeping me going. I would have 3-4 cups a day with skim milk and splenda… yea.

When I finally learned a little bit a bout the possible negative side effects of coffee, not even as they pertain to autoimmune disease (see below under “other considerations”), I thought I should maybe see what happens when I come off it. I thought it might helps some of the anxiety and depression that I continued to battle post- “recovery” from celiac disease (I put “recovery” in quotations because even though I got back to a healthy weight after going gluten-free I had NOT really recovered). When I made the switch to green tea, I noticed my anxiety levels drop, A LOT, and I vowed never to go back…. and yet. I went back. Don’t ask me how or why. It just happened!

I never quite jumped back to my 3-4 cups daily, but I definitely would have one every morning (now with almond milk and raw honey) and I thought it was totally fine. Then, I hopped on board the bulletproof train because I wanted to experiment with supported intermittent fasting. I thought this made me feel like a superstar! Until, it didn’t. The coffee and MCT oil every morning definitely gave me an energy boost but I was starting to feel the anxiety come back full force. I was getting jitters and began to feel out of control. I switched to bulletproof Matcha for a time and I experienced the same relief. My anxiety dropped right off and I felt energized and focused without coffee. I swore I would never go back… and yet…

I was back on bulletproof coffee for some time before I started to notice that my bowels were starting look like they used to in the bad ol’ days of peak celiac…. well, maybe not quite as bad but they were very very loose and I would see the occasional piece of food and mucous, which FYI is NOT OK! If you see food or mucous in your stool, please consult a health care practitioner.

I was scared enough by seeing my bowels go so far off with no apparent trigger that I decided it was time to implement the full autoimmune protocol (AIP). The first time I did AIP, I followed the elimination phase for 5 weeks… and then I went on a cruise with my family and had coffee every day amongst many other elimination illegal foods and never really did a proper reintroduction. Womp womp. I was back on the coffee train and didn’t have any further answers but had done enough gut-healing during the elimination phase that my bowels were back on track and I wasn’t worried. I just stayed full paleo and ate the “elimination” foods less frequently… except for coffee, which I had (with collagen to justify it in my head) every single day.

It wasn’t until the second time I did the AIP protocol that I finally took the time to do proper reintroductions and monitoring of symptoms. Even though it’s not supposed to be, coffee was one of my first reintroductions. Why? I have no idea. I don’t even like it that much… I think it’s a little bit about wanting to get coffee with friends and fitting in. I don’t know. Alas, I reintroduced coffee early AND… I felt AMAZING!!! Perhaps a touch overboard, like out of control happy and excited and energetic, but at the time I thought that was awesome! I felt great the second time I had it, and the third time, but the fourth… the fourth pushed me over the edge. I was feeling great at first, I had a super productive day and I was full of energy. I walked home that day and grabbed a few groceries on my way. Silly me, I had forgotten my reusable bags so I grabbed a plastic bag (sorry world!). I got about 5 meters from my front door before the plastic bag snapped and my avocados rolled onto the street and got run over by a passing truck. I… LOST IT! And not in a grumbling to myself and venting to my husband kind of way. I literally fell to ground, screamed and wept. THIS IS NOT NORMAL. For a small trigger to bring you from your best to your worst day ever is NOT normal.

In the end, it is my conclusion that, as you probably could have told me after reading my first paragraph, I CANNOT do coffee every single morning. My adrenals are not strong enough to deal with that level of excess cortisol secretion and it leaves me unable to handle stress. It is unlikely that coffee caused my initial relapse in digestive disturbances, but after doing proper reintroductions on the autoimmune protocol (AIP) I have identified it as a trigger for my adrenals at least and that is something I do not want to mess with given that my system is so sensitive and this has implications for my autoimmune diseases. It was not until after discovering my issues with coffee that I was finally also diagnosed with Hashimoto’s Thyroiditis, which can very much affect adrenal function and vice versa.

I still consume a really good coffee on occasion, but I usually throw in adaptogens like Maca and load it up with anti-inflammatory agents like Turmeric to even out it’s effects. Otherwise, I’m a Matcha girl for life!

Now enough about me, you probably want to know how coffee might be affecting YOU and your autoimmune disease right?!

Well, put on your scuba gear, cause we’re about to take a deep dive!

Coffee & Your Immune System

Coffee & Your Immune System

Although coffee may boast many benefits including reduction in all-cause mortality, lower risk of death from digestive diseases and reduction in circulatory diseases, as someone with autoimmune disease I have to look at things a little bit differently. My first questions is always, how does this affect my immune system?

Scientific evidence clearly shows that coffee can have dramatic effects on the immune system, but they are complicated and vary from person to person. This suggests that there is a genetic component to how coffee interacts with your immune system!

Generally, caffeine seems to promote anti-inflammatory action on many components of the immune system. However, there are still several studies that link coffee consumption to higher inflammation levels! In one key study, moderate coffee consumption in healthy subjects correlated with increased markers of inflammation. They had higher levels of C-reactive protein (CRP), serum amyloid-A and white blood cell counts. In people who drank high amounts off coffee (over 200 mL daily), they observed an increase in circulating white blood cells and inflammatory cytokines (chemical messengers of inflammation), such as IL-6 and TNF-alpha. But again, other studies have observed the exact opposite!

When looking at coffee or caffeine’s effects on specific immune cell types, we also see varying results. Some studies suggest a suppression of neutrophils and monocytes, two key cell types of the innate immune system (your first-line defense), which could indicate anti-inflammatory effects. Meanwhile, other studies reveal increased endothelial dysfunction related inflammation biomarkers, including endothelial adhesion molecules, which stick to the outer cell membrane and interact with adhesion molecules on white blood cells to allow them to move from the bloodstream into the tissues. White blood cells concentration in certain tissue leads to inflammation at the site.

Caffeine intake appears to suppress proliferation of Th1 and Th2 cells, key to the adaptive immune system. As many of you likely know, if you have autoimmune disease, these are major drivers of inflammation for us. But before you jump for joy and chug your second cup of coffee, we must also consider that caffeine seems to also suppress Th3 cells, which are important regulatory T-cells that control the balance of the immune system.

Caffeine may also suppress the function of B cells, leading to a reduction of antibody production. Again, sounds amazing for those of us with autoimmune disease. However, when we look at coffee as a whole, the galactomannans found in the beans may have immunostimulatory effects that increase the activity of both B cells and T cells.

Furthermore, coffee intake may also impact cell signalling. NF-kB is a protein complex that control cytokine production and is an incredibly important part of the intestinal immune system. Hello, my celiac and IBD friends! This bit is for you! Chronic activation of NF-kB is particularly highly associated with IBD and celiac disease, although it is implicated in all autoimmune and chronic inflammatory conditions. Studies would suggest that coffee induces activation of NF-kB in intestinal epithelial cells (the cells of the gut lining), intestinal endothelial cells (cells of the capillaries) and in macrophages.

Again, some studies have shown just how variable these results are from person to person. A particular study looked at the blood of the participants before and after coffee consumption and observed what would happen after introducing an inflammatory stimulus. The used a mass spectrometer to measure the reactions of inflammatory mediators like cytokines, chemokine and aicosanoids. They observed that in the majority of individuals coffee consumption caused significant downregulation of most inflammatory markers, in others the exact opposite effects were observed.

Still confused? SO AM I! It still seems there is no definitive answer as to whether coffee is going to inflammatory or anti-inflammatory for you. What we do know, is that there are definite interactions with the immune system and that your reaction likely depends, in large part, on genetics. This, in itself, is a really great reason to do the AIP elimination and pay very close attention to your reaction to coffee upon reintroduction. However, we may have a few clues as to which genes might make you vulnerable to coffee intolerance.

Coffee and You Genetics

Coffee & Your Genetics

Have you ever seen your friend order an espresso after dinner and wonder how the heck she’s going to get to sleep that night? She may well sleep like a baby after that, while you would be up all night tossing and turning if you had one! Why is that? Genetics! The CYP1A2 gene controls the cytochrome P4501A2 enzyme, which is responsible for nearly all of our metabolic processing of caffeine. There are two possible variants of the gene. The CPA1A21A allele results in fast caffeine metabolism (your friend who can have espresso after dinner and sleep sound an hour later), and the CPA1A2*1F allele results in slower caffeine metabolism (you tossing and turning at night after just a sip of coffee at 2pm)!

That is just one example of how genetics affects our reaction to coffee. But how does our genetics link to autoimmune disease and coffee intolerance? There are two specific genes that have become of particular interest.

NAT2 polymorphisms

This is an enzyme involved in the metabolism of coffee and other foreign substances that we ingest. Specific polymorphisms lead to slower acetylation, resulting in slower degradation of toxic intermediates (molecules created during the metabolism of the substance. A slower acetylation rate can aggravate autoimmune disease processes due to the prolonged exposure to these toxic by-products. Therefore, people with the NAT2 polymorphism that causes slower coffee acetylation may worsen their risk for autoimmune disease or contribute to the progression of a pre-existing disease by regularly consuming coffee.

HLA genes

Human leukocyte antigen (HLA) genes are another gene implicated in autoimmune disease and holds a connection with how we react to coffee consumption. There are two HLA haplotypes (I and II), and haplotype II has been implicated in autoimmune disease due to it’s influence on T helper cells and regulatory T cells. HLA II is particularly well linked to rheumatoid arthritis, type 1 diabetes mellitus and Grave’s disease. The connection to coffee consumption comes from a recent study that suggests that coffee consumption may increase the risk of autoimmune diabetes in adulthood for people with HLA II genes.

You can find out if you have any of these gene variants by conducting genetic testing like 23 and me. This may be a useful tool for those of us with autoimmune disease to understand whether coffee is a helpful or not so helpful choice.

Coffee and Digestion

Other Considerations


Cafestol and kahweol, two compounds found in coffee, may have cholesterol-raising effects, leading to higher LDL and total cholesterol.

Digestive Distress

Many people notice either digestive upset or heartburn when they consume coffee. This is likely because coffee stimulates the secretion of gastric juices and stimulates peristalsis (the contraction of your gastrointestinal muscles that move substances through the digestive tract). This is generally why we feel coffee helps us go to the bathroom.

Coffee also promotes the release of cholecystokinin (CKK), a hormone that stimulates the release of bile from the gallbladder. In a healthy individual, this release of bile will neutralize the highly acidic chyme (broken down food and/or liquid components from the stomach that have become extra acidic because of coffee’s stimulation of stomach acid). However, in the case of impaired gallbladder function or excessive coffee consumption, this highly acidic chyme may enter the small intestine unneutralized and create irritation and inflammation of the gut lining.

Adrenal Impact

As I mentioned breifly in my introductory thoughts, I often recommend that people with autoimmune disease, especially those in which hormones are impacted (ie. Hashimoto’s, Endometriosis, and especially Addison’s Disease), come off of coffee for a time due to the impact on the adrenals.

Caffeine stimulates cortisol secretion by elevating the production of adrenocorticotropic hormone by the pituitary gland. Excessive cortisol production can lead to an overactive immune system (inflammation & autoimmunity), disrupted sleep, impaired digestion, depression and hormonal imbalance.

When we consume coffee, our cortisol increases and may stay increased for up to 6 hours. If you drink coffee every single day, you will also likely experience a more dramatic increase of cortisol in response to stress over time. This means your cup of coffee in the morning might be contributing to that road rage on your way to work and keeping you on edge all day. If you have a hard time managing stress already, it might be a good idea to ease up on the coffee. Keep in mind, going cold turkey may be difficult on your adrenals to re-adapt to their own regulation of cortisol. I recommend coming off of coffee in a slow and controlled manner.

Coffee and Autoimmune Disease

So… I don’t need to give up coffee, right?

I think when we look at the research, the only thing that is clear is that coffee can have drastic effects on your health but those effects really are different for every person. It depends in large part on your genes, and if you’re someone with autoimmune disease we may be able to provide more insight based on specific studies that look at coffee consumption as it relates to your particular disease.

For example, there is some evidence that there is an increased risk for the development of rheumatoid arthritis amongst coffee-drinkers. This would suggest that if you already have RA, coffee probably is not helpful in trying to manage disease progression.

As mentioned before, drinking more than 4 cups of coffee a day may increase the risk of developing late-onset autoimmune type 1 diabetes mellitus, particularly in those with HLA II genes. Again, I would suggest if you already have type 1 diabetes, coffee consumption may not be ideal as there have been studies further correlating coffee consumption with episodes of hypoglycaemia and up to a 15% reduction in insulin sensitivity.

On the other hand, coffee consumption is inversely associated with the development of multiple sclerosis as well as IBD (ie. Crohn’s disease and ulcerative colitis). This would suggest it may help to prevent and slow disease progression.

For those with celiac disease, like me, the topic can be tricky because coffee has been demonstrated as a gluten cross-reactor. This means that we may create the same inflammatory reaction & destruction of the intestinal tract that we would if we consumed gluten when we consume coffee. However, the research tends to indicate that quality is key. Espresso, Turkish and Israeli coffee beans tend to be less reactive, while instant coffee can be extremely reactive. Some people with celiac disease may not experience full recovery unless they cut coffee out altogether. As I always say, it’s a little bit more complicated than just going gluten-free.

At the end of the day, we really just need to figure it out for ourselves. I don’t know how many times I’ve said it in this article alone but EVERYONE IS DIFFERENT and, as you can see, there are SO MANY factors that dictate how your body will respond to the myriad of compounds, from caffeine to galactomannans in coffee. So, my advice? Take what you can from the information given above. Maybe try out some genetic testing to give you a better guess. But first and foremost, LISTEN TO YOUR BODY!

Again, the best way to really tune in to how your body reacts to coffee may be to try an elimination protocol, like AIP and pay attention to how you feel when you reintroduce it. Look for inflammation showing up in skin, joints, muscles, anywhere! Pay attention to your stress responses, energy levels, mood, cravings, bowel movements, gas, bloating and any pain at all (including headaches!). These can all help to pain a picture of how coffee is affecting you. No symptom is too small to give you a sign that something is up. Listen closely and honour your body.

If it turns out coffee isn’t your friend, do not fret! There are so many comforting alternatives to coffee. Check out my blog on Loaded Lattes to help get you started!

As always, I’m here for you. Feel free to reach out via the comments section below or contact me individually to ask questions or discuss your concerns.

Kisses & Kombucha…er Coffee?,


Coffee: Good or Bad?


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