grab my *free* Starter Kit:

3 daily habits that improve
leaky gut and autoimmunity!

I want it!

The Truth About Coffee & Gut Health

Filed Under:

Is coffee actually good for us, or is it secretly wreaking havoc on our health? And what about its impact on our gut health? Here’s the truth about coffee: the good, the bad, and the downright confusing.

truth about coffee

Reading Time: 10 minutes

Coffee isn’t just a drink; it’s practically a cornerstone of modern American life. You’d be hard-pressed to find someone who doesn’t indulge in at least one cup a day. But for many of us, coffee is more than just a caffeine fix—it’s a ritual, a social experience, and a journey through a world of rich flavors. It’s like exploring a whole pallet of taste, much like foodies with their meals or wine lovers with their bottles. But amidst all the enjoyment, there’s always that nagging question: is coffee actually good for us, or is it secretly wreaking havoc on our health? And what about its impact on our gut health? 

Well, here’s the scoop: the good, the bad, and the downright confusing truth about our beloved brew.


Coffee consumption can affect the body in multiple ways, including physically, mentally, and emotionally. First and foremost, coffee contains caffeine, which stimulates the central nervous system. As caffeine enters the bloodstream, it travels throughout the body and crosses the blood-brain barrier. It blocks adenosine, a neurotransmitter that is responsible for making you sleepy. Hence, the physical energy-boosting effect of coffee. 

Simultaneously, caffeine can also increase levels of dopamine and norepinephrine. This boost can improve your mood. According to Harvard, dopamine is linked to love, pleasure, motivation, and the brain’s reward system. It also aids in memory and learning abilities. Turns out, coffee is more than a pick-me-up, it also serves our brain!


Drinking coffee on a regular basis comes with its own benefits and drawbacks. To start with the good news, coffee can potentially benefit your health! Here’s how:

truth about coffee benefits
Dopamine and Norepinephrine

Dopamine and norepinephrine are neurotransmitters in the brain responsible for regulating mood, pleasure, and cognitive function. Dopamine, often termed the “feel-good” neurotransmitter, influences motivation, and various brain functions including memory and attention. Norepinephrine plays a role in the body’s stress response and helps regulate attention and alertness. When caffeine from coffee stimulates the release of these neurotransmitters, it leads to increased alertness, improved mood, and enhanced cognitive function, explaining why coffee consumption is associated with feelings of energy and mental clarity.

Cognitive Function

Drinking coffee is known as a pick-me-up beverage, due to it’s ability to increase alertness, cognitive function, memory, and coordination. It may even lower the risk of Alzheimer’s disease and Parkinson’s disease. One study shows this is likely due to the various compounds found in roasted coffee beans, such as quercetin and phenylindanes.

Anti-Inflammatory Properties

Coffee is rich in antioxidants, notably polyphenols, renowned for their anti-inflammatory properties. Chlorogenic acids, a prominent type of polyphenol found in coffee, has significant impacts on cardiovascular, metabolic, and neurological health. Their potent anti-inflammatory effects make them invaluable in combating chronic diseases, contributing to your overall health. Enjoying your morning coffee not only provides a stimulating start to the day but also delivers a substantial dose of health-promoting compounds, bolstering your body’s defenses against illness.

Magnesium Content

Coffee is rich in magnesium, the master mineral. Magnesium is quickly depleted by stress of any kind (physical, emotional, or mental), making it an important mineral to intentionally replenish. Magnesium is responsible for more than 300 enzymatic reactions in the body and greatly supports liver function– both of which are critical for overall health and well-being.

Glucose Regulation

Glucose regulation is exceptionally important in metabolic health and fighting metabolic diseases, such as Type 2 Diabetes. The protective benefits of coffee “can be related to the content of bioactive compounds, such as CGA, trigonelline, lignans, quinides, cafestol and kahweol, that possess anti-inflammatory properties,” according to one study.

Gut Stimulant

Coffee is more than just a morning eye-opener; it’s also a reliable gut stimulant, known to kickstart gut motility and keep things moving smoothly. This not only helps maintain regular bowel movements but also plays a crucial role in detoxification, flushing out toxins and preventing the discomfort of constipation. By warding off constipation, coffee also helps mitigate the risk of potential complications such as bacterial overgrowth and the accumulation of toxins in the body, ensuring our digestive system stays in top-notch condition.

While it’s undeniable that coffee offers a plethora of noteworthy health perks, it’s essential to acknowledge that it also carries its own set of drawbacks. But don’t worry! By diving deeper into the nuances of coffee consumption, we can navigate the potential pitfalls and have a clearer understanding of how to optimize its benefits while mitigating its adverse effects. Let’s understand the intricacies of coffee’s impact and learn how to sidestep the less desirable aspects, ensuring our coffee experience remains as positive and beneficial as possible.

coffee and leaky gut

When drinking coffee, there are a few considerations to keep in mind (AKA “the bad”):

Cream and Sugar

When it comes to sweetening your coffee, tread carefully with cream and sugar. Overindulging in these additives can send your blood sugar levels on a rollercoaster and contribute to inflammation, potentially disrupting the delicate balance of bacteria in your gut. Also, the inclusion of cream introduces dairy into the mix, a known culprit for triggering autoimmune responses and gut-related issues in some individuals. So, while a touch of raw heavy cream and natural sugars may add flavor, it’s crucial to exercise moderation to safeguard both your blood sugar levels and gut health in the long run. 

Healthier alternatives for sweetening your coffee can look like manuka honey, or organic maple syrup! Mix it together with some A2 raw cream, raw dairy milk, coconut milk, or even goat milk!  With these healthier additions, you’ll be well on your way to a much better cup of coffee! 

Afternoon Coffee

Indulging in an afternoon coffee, typically anytime after 12pm, can disrupt your circadian rhythm and cortisol, potentially resulting in suboptimal sleep quality and reduced REM sleep. This timing can interfere with your body’s natural sleep-wake cycle, making it harder to fall asleep and stay asleep throughout the night. As a result, while a midday pick-me-up may offer temporary alertness, it’s essential to be mindful of its potential repercussions on your sleep patterns.


Hydration is key, and it’s important to recognize that coffee, being a natural diuretic, can draw water from the body, potentially leading to dehydration. This can manifest as fatigue, brain fog, increased food cravings, and headaches. When we’re not properly hydrated, our bodies struggle to function optimally, impacting both physical and cognitive performance. While coffee can provide a temporary energy boost, it’s essential to balance its consumption with adequate water intake to ensure you’re not putting your body at a disadvantage. 


Unfortunately, coffee does come with it’s own dangers (AKA “the ugly”). These dangers aren’t fatal, but they can worsen chronic conditions and decrease your quality of life. 

truth about coffee and health

When it comes to coffee, it’s crucial to be aware of potential toxin exposure. Shockingly, many coffee beans harbor toxins, including mycotoxins, which are notorious byproducts of mold. Additionally, coffee ranks among the most heavily pesticide-treated crops, leaving beans laden with harmful chemicals and heavy metals. Given the extensive processing and transportation involved in coffee production, these contaminants can pose significant health risks if not properly addressed. Prioritizing high-quality, organically sourced coffee can help mitigate exposure to these harmful substances and safeguard your health.

Stress Response

Coffee is a stimulant, which triggers our body’s natural fight-or-flight stress response. This response releases our stress hormones, like adrenaline and cortisol, and can contribute to a dysfunctional nervous system. Consistently triggering our fight-or-flight response can cause restlessness and increase anxiety or panic attacks.

Autoimmune Flare Ups

The research on coffee and autoimmunity is a bit controversial and it really depends on many factors. In some individuals, coffee can increase inflammation. It can also interfere with how the body absorbs certain nutrients from food. In addition, coffee may mimic gluten for some people with Celiac disease due to molecular mimicry and trigger a reaction. For individuals currently in an autoimmune flare and those trying to reverse autoimmunity and improve symptoms, it is best to avoid coffee. 

Gut Flare Ups

For individuals grappling with conditions such as irritable bowel syndrome (IBS) or other chronic digestive ailments, the effects of coffee can be a double-edged sword. While heightened gut motility can be beneficial for some, especially in aiding regularity, it can also exacerbate symptoms of IBS. The increased motility induced by coffee may trigger distressing symptoms such as diarrhea and abdominal pain, leading to uncomfortable flare-ups. Understanding the full impact of coffee on digestive health is so essential for managing these conditions effectively and minimizing discomfort.

Adrenal Fatigue

When our bodies enter into the fight-or-flight mode, our adrenal glands kick into high gear to produce increased amounts of cortisol, our stress hormone. This heightened production can potentially result in a condition known as Adrenal Fatigue or HPA-Axos Dysfunction. For individuals already grappling with Adrenal Fatigue, regular consumption of coffee can further strain the adrenal glands, hindering their ability to recover and exacerbating symptoms. Therefore, while coffee may provide a temporary energy boost, it’s crucial to consider its impact on adrenal health for those navigating adrenal fatigue.


Although coffee comes with it’s own good, bad, and ugly, it is possible for most to enjoy coffee in a healthy, moderate way. Follow these tips to reap the health benefits of coffee without the negative side effects:

truth about coffee and gut health and autoimmunity
Coffee With or After Eating

Having coffee with or after a meal can be so beneficial for digestion and minimizing potential GI discomfort. When coffee is consumed alongside food, it helps to neutralize its acidity, reducing the risk of digestive issues like acid reflux. Plus, having coffee with a meal slows down its absorption, preventing sudden spikes in blood sugar and providing a more sustained energy boost. Drinking coffee AFTER eating can help kick start digestion, ease bowel movements, and alleviate that feeling of post-meal sluggishness. 

Avoid Dependency

To prevent dependency on caffeine, I recommend alternating between regular and decaf coffee. Incorporating periods of consuming only decaf coffee provides your nervous system with much-needed respite from the stimulating effects of caffeine. This approach not only helps regulate your caffeine intake but also offers a chance for your adrenal glands to recover and function better. By maintaining this balance, you can enjoy the ritual of coffee without relying solely on its caffeine content, and promote your adrenal health at the same time!

Choose High Quality Coffee

When selecting your coffee, prioritize high quality options that are free from pesticides, mold, heavy metals, and other harmful toxins. Look for brands that prioritize organic and sustainable sourcing practices to ensure both the quality of the coffee and the well-being of the environment. 

One outstanding brand that meets these criteria is Purity Coffee. Their commitment to quality is evident in their rigorous third-party testing process, guaranteeing that every cup meets the highest standards for no mycotoxins or heavy metals. 

Another exceptional choice is Organo Gold coffee. What sets Organo Gold apart is its unique addition of Ganoderma lucidum, a medicinal mushroom with a long history of health benefits. Ganoderma adds an extra layer of richness and depth to the coffee’s flavor profile, while also offering potential gut and autoimmune health perks such as immune support and increased energy. 

By choosing brands like Purity Coffee and Organo Gold, you can savor your coffee with confidence, knowing that you’re enjoying a high-quality brew that’s both delicious and beneficial for your health.

Make a Gut-Healthy Coffee- Coffee can be made in a way that supports your blood sugar and gut microbiome. Check out my favorite gut-healthy coffee recipes to support your health, while enjoying your morning cup of Jo without dairy. Here’s two that I really love! 

gut healthy coffee
Bulletproof Style 

Health Benefits: Add MCT oil to your coffee to create a Bulletproof style coffee. MCT oil helps regulate your blood sugar to keep you fuller longer. It also provides healthy fats to boost brain function and balance hormones.

Recipe: Combine 6-8 oz of brewed Purity coffee with 1 tbsp gelatin + 1 tsp Fourth & Heart ghee OR 1 tbs MCT oil. Blend for 60 seconds in Vitamix or high speed blender. Pour into mug and enjoy

Coconut Cream Latte

Health Benefits: I recommend using Native Forest Plain and Simple Coconut Milk because it is free of binders, fillers, and gums (which can often cause digestive distress). Nutiva only contains coconut meat/cream and filtered water. Score!

Recipe: Shake the Nutiva can before opening. Once open, stir well to mix the liquid and cream (liquid naturally settles on the bottom and cream collects on top). Then, add ¼ cup to a heated milk frother (like this one). Alternatively, you can find an inexpensive, yet effective handheld frother from Amazon, HERE. After frothing, pour the milk into a mug with coffee and sprinkle with cinnamon

You can also shop my favorite coffee products, here.

Stay Hydrated

Ensuring proper hydration is essential when enjoying your coffee. Be sure to maintain hydration levels by drinking plenty of filtered water throughout the day, especially alongside your coffee intake. It’s a good practice to start your day with a glass of water before reaching for your cup of coffee, as this helps replenish fluids after a night’s rest and primes your body for optimal hydration. 

Avoid Coffee During Active Flares

When dealing with an active autoimmune flare, it’s crucial to steer clear of coffee and all caffeinated beverages, as they may exacerbate symptoms. Instead, opt for coffee alternatives that are AIP-friendly. 

Chicory Root Coffee is an excellent choice in such situations. This beverage offers a rich, coffee-like flavor without the caffeine content found in traditional coffee. Chicory root contains inulin, a prebiotic fiber that supports gut health and nourishing beneficial gut bacteria. With its earthy taste and digestive benefits, chicory root coffee serves as a comforting and supportive option if you’re following an autoimmune protocol.


Coffee is undoubtedly a beloved morning staple, offering not only a delightful taste but also potential health perks. Yet, to truly reap the benefits of this cherished beverage, it’s vital to approach coffee consumption with care and consideration for our well-being. 

By incorporating these guidelines into our coffee routine—such as opting for high-quality options, ensuring adequate hydration, and making mindful choices during health challenges like autoimmune flares—we can strike a balance between enjoying our coffee and safeguarding our health. Let’s remember these simple strategies as we enjoy our good old cup o’ joe! Happy drinking!

What is your favorite way to drink coffee? Let me know below! 

truth about coffee and gut health

Leave a Reply

Your email address will not be published. Required fields are marked *

"When it comes to balancing our body, healing the gut, reversing autoimmunity, and achieving optimal health—we are a lot like a car that won’t run right. In order to fix the problem once and for all instead of relying on jumper cables, we must get underneath the hood, run the diagnostics, and replace the battery so that it runs good as new."

-Nikki Yelton, RD

a note from nikki:

If you are ready to stop wasting precious time, get off the never-ending hamster wheel, and finally surrender trying to figure things out on your own—this is your moment. 

You don’t have to settle for just getting by and hoping tomorrow is a better day. We both know you are a woman who deserves better and are made for so. much. more.

are you ready?

Ready to resolve your GI distress, reverse autoimmunity, and live your extraordinary life?


start your journey

I believe every woman can take back their health

hey there!