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The Impact of Coffee on Gut Health: What Does the Science Say?

Updated: Jun 9

cup of coffee

What are the effects of coffee on the gut microbiome?


Coffee (or caffeine) is probably the most loved psychoactive drug in the world, and until recently it was largely believed to be potentially harmful to our health. Previously, studies have shown contrasting results, however, an increase in recent research is starting to reveal otherwise, in terms of its' effect on various chronic health conditions, with some studies also linking it to a healthier gut microbiome.

Coffee is made from coffee beans, which are actually seeds, that are naturally green when harvested. The drying and roasting process makes them into the chocolatey-brown beans that we know.

Like most plant foods, the coffee beans (or seeds) are rich in phytochemicals (plant chemicals), specifically antioxidants, polyphenols, and also some fibre (in lower amounts).

Polyphenols are natural compounds that have anti-inflammatory and antioxidant benefits and help to increase the diversity of our gut microbial population. This is because they are thought to have a prebiotic effect on the gut microbes.

Many plant foods are rich in polyphenols and antioxidants, specifically berries, cacao (or dark chocolate), coffee, spices, particularly cloves, nuts and seeds, olives, extra virgin olive oil, plums, cherries, green tea, and black tea.


Phenols are a large group of chemical compounds naturally found in plants, and found in foods in the form of polyphenols. There are more than 8000 different types of polyphenols, some specific examples include phenolic acid, stilbenes, lignans, flavonoids, flavanols, quercetin, catechins, anthocyanins, and cyanidin.


The gut microbiome is a complex and diverse ecosystem of trillions of microorganisms such as bacteria, fungi, viruses, and archaea, that influences our health in a multitude of ways, specifically our vital nutritional, metabolic, and immune functions within the body.

In general, coffee consumption can also be beneficial for the digestive process, as its bitter compounds helps to stimulate gastric acid secretion, bile and pancreatic enzyme secretion, and the stimulation of motility. Furthermore, it can reduce the risk of gallstone formation.

Nevertheless, coffee might be best avoided by people with gastroesophageal reflux disease (GORD), peptic ulcers, and other intestinal inflammatory diseases (1).

A review of the evidence showed one very small study of 16 healthy adults drinking 3 cups of coffee a day for 3 weeks found increases in Bifidobacterium spp. which was thought to be due to the polyphenols.

Other studies showed that long-term consumption of 7 cups of coffee a day was associated with a decreased risk of T2DM, obesity, and metabolic syndrome. Although this evidence was difficult to extrapolate because cup size could vary between 150ml and 300ml.

Research has also shown benefits in general for liver disease prevention (2), as well as heart disease, T2DM, and Parkinson’s prevention (3).


heart-shaped coffee beans

Photo credit: Dominka Roseclay

What are the long-term Gut health benefits of drinking coffee?


Firstly, it depends. There’s no one-size-fits-all when it comes dietary advice, and this includes coffee consumption. We’re all genetically individual, therefore, we will all respond differently. And especially when it comes to the gut microbiome because it will depend on the health of each individual’s microbiome (as they are all unique).


It also depends on how much coffee is being consumed. Extrapolating the evidence from research can be tricky, as in the case of coffee, it rests so much on how it is prepared, how it is consumed, how much is consumed, what else is added to it (sugar, milk etc.), and what the person’s diet is like in general.


One relatively small study of 147 healthy controls, from 2020 (4), found that regular coffee consumption (up to 500ml/day) showed higher faecal levels of Bacteroides, Prevotella, and Porphyromonas species, which are often low in people with impaired health conditions, however, no differences were detected in the faecal levels of short-chain fatty acids (SCFAs) (4).

Other research (in mice) has shown higher levels of Faecalibacterium, a butyrate-producing bacteria, which is generally considered a beneficial bacteria. The polyphenols in coffee were attributed to the gut health benefits.

Another small study from 2019 (5), (34 participants), examined the effects of caffeine consumption on the colonic mucosa and the gut microbiome. They found that a higher caffeine consumption was associated with an increased richness and diversity of beneficial bacteria, and lower levels of potentially harmful bacteria.


What are the adverse effects of drinking coffee and how wary should we be of caffeine?


Caffeine is a central nervous system stimulant so it can help us to increase our performance. Caffeine stimulates the release of adrenaline and dopamine, which has beneficial effects such as increasing our alertness and focus, increased pain tolerance, and reduces fatigue. It also increases our metabolism, which could be beneficial for some people, although not everyone.

However, some negative effects include:

  • Anxiousness and spikes in our heart rate (which can lead to a feeling of 'the jitters'), and too much coffee can be a cause of insomnia.

  • There are certain genetic variants, known as single nucleotide polymorphisms (or SNPs), which can increase our sensitivity to caffeine (ADORA2A), meaning that it could be significantly more stimulating to someone with these genetic variants, than someone without them.

  • Other SNPs can also mean that those people affected have slower detoxification pathways, which could result in headaches. And because caffeine is metabolised in the liver, certain genetic variants (such as CYP1A2), are associated with a faster or slower metabolism of caffeine.

  • If you’re a slow metaboliser, it’s best to limit your caffeine intake to earlier in the day, and preferably before noon, but also consider body size, as well as how much caffeine your body is used to, as we can become desensitised to it.

  • Coffee has been negatively associated with adrenal issues, especially for people who have been under a lot of stress, and it could worsen anxiety in those who are susceptible.

  • Furthermore, for those who suffer with acid reflux or an intolerance to histamines, it’s probably best avoided.

  • As coffee is a diuretic, we need to ensure that we are drinking plenty of water or herbal teas alongside, to prevent dehydration.

  • Coffee can have some interactions with certain medications (for instance, thyroid medication), therefore, it’s always best to get this checked out with a health professional, as it may be reducing the effectiveness of your medication.

  • Coffee consumption could be associated with unwanted side effects of increased anxiety, which may be especially noticeable for some women going through hormone changes such as peri-menopause and menopause.

  • Coffee can be a useful addition for people with sluggish bowels or constipation, but it could be not so helpful for someone with anxiety (as it could worsen) and cause loose stools (or diarrhoea). 

  • Coffee might be best avoided by people with gastroesophageal reflux disease (GORD), peptic ulcers, and other intestinal inflammatory diseases (1).

Getting your caffeine from natural sources like coffee, tea, and cocoa beans is always preferable to carbonated energy drinks or pharmaceutical products.

Best types of coffee to drink


If you are a coffee lover, I’d always recommend drinking organic fair trade coffee such as Exhale Coffee (mycotoxin and mould free), Grumpy Mule, Tugboat, or Waitrose (Sumatra, Mach Pichu, and Colombia).


If you’re including cow’s milk, then choose organic, ideally full fat. If you’re opting for a plant milk, then make sure to use one with minimal ingredients, preferably only 2 or 3 maximum (e.g. nuts/oats, water, and sea salt), or make your own.


And be careful with the sugar. We know sugar can cause imbalances in blood sugar and can contribute to weight gain. It’s also not great for the gut microbiome.



If you love coffee but you're prone to anxiety or getting 'the jitters', you might want to consider an adaptogenic or mushroom coffee – London Nootropics (with 20% discount), or Solve.


cup of adaptogenic coffee


Helen Ross is a Registered Nutritionist ® specialising in gut health and IBS support. If you'd like to know more about eating for a healthy gut, or lifestyle tips for keeping your gut healthy, book in for a FREE call here to discover how she can help you. 

Helen offers a virtual (online) clinic and IBS support and nutritional therapy services locally to the Bridport, Dorchester, Weymouth, Poole, Bournemouth, and East Devon areas. 

My Simple Gut ReSet is designed to help us get to the root cause or causes of your health issues. The aim is to nourish and support the gut lining to assist it back to a healthy state. A robust intestinal lining is an essential first step for finding freedom from painful, frustrating and embarrassing symptoms of IBS and other gut-related symptoms and health problems.

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