For millions of people, the day begins more or less in the same way: coffee, possibly before having to speak to someone. Caffeine does its job and makes us more alert, we know this. But coffee contains hundreds of other substances and in recent years research has realized that that daily cup seems to leave traces much further from the brain.
The interesting part is that not everything coffee does – or seems to do – depends on caffeine. Some effects have also been observed with decaffeinated coffee, involving polyphenols, chlorogenic acids and the interaction with the bacteria that inhabit our intestines.
Before transforming the moka into a health device, however, caution is needed. Many of the most spectacular results come from observational studies: they tell us that two phenomena often appear together, not necessarily that one causes the other.
Coffee modifies the intestinal microbiota
One of the most recent clues comes from a study published in Nature Communicationsin which researchers compared 31 regular coffee drinkers with the same number of people who didn’t drink coffee. The former then eliminated coffee for two weeks and reintroduced it for 21 days, in the normal or decaffeinated version.
The composition of the microbiota changed during the different phases of the experiment and some variations reappeared with both caffeinated and decaffeinated coffee. The sample is small, so we are very far from being able to say that coffee “settles the intestine”, but the data suggests that other substances present in the drink also interact with our intestinal bacteria.
It’s not even the first clue. In 2024, research on over 22 thousand people found a much greater presence of Lawsonibacter asaccharolyticus. Furthermore, in the laboratory, coffee favored the growth of the bacterium. The researchers identified a total of 115 microbial species positively associated with coffee consumption. What exactly these differences mean for our health is yet to be understood.
It makes you more alert, but can take its toll on sleep
Here the mystery is decidedly less. Caffeine temporarily blocks adenosine receptors, a substance that accumulates throughout the day and contributes to feelings of drowsiness. Result: attention and vigilance increase and tiredness is perceived less. It doesn’t mean that the body suddenly produced energy out of thin air. Simply, the signal of tiredness comes with less force.
And it’s also why time matters. According to the European Food Safety Authority, even a single 100-milligram dose of caffeine can affect the length and quality of sleep in some people if taken close to bedtime. Individual sensitivity, then, changes a lot: someone can drink an espresso after dinner and fall asleep peacefully, someone else after a coffee at four in the afternoon stares at the ceiling until two in the morning.
The association with type 2 diabetes also appears with decaffeinated coffee
Among the most consistent results is that on type 2 diabetes. A meta-analysis published in Diabetes Care brought together 28 prospective studies for a total of over 1.1 million people.
As coffee consumption increased, the risk of developing type 2 diabetes statistically decreased. In the group that consumed six cups a day, the relative risk was 33% lower than in those who did not drink coffee or consumed it very rarely.
No, this is not an invitation to drink six. The studies are observational and the meta-analysis itself recognizes the possibility of confounding factors. The interesting detail is another: the association appeared for both normal and decaffeinated coffee. Again, caffeine doesn’t explain everything.
The liver also seems to have a particular relationship with coffee
The liver is probably the organ for which the associations observed in coffee studies are most surprising.
A meta-analysis published in BMJ Open, which included more than 2.2 million participants in cohort studies alone, found that two extra cups of coffee per day were associated with a lower relative risk of hepatocellular carcinoma.
Another systematic review on cirrhosis observed a similar pattern: two additional daily cups were associated with a lower relative risk of cirrhosis.
Here too the correct verb remains “associate”. We don’t know if coffee directly produces the effect and it wouldn’t make sense to use it as a treatment for liver disease. The fact that similar results appear repeatedly in different populations, however, has made the relationship between coffee and liver health one of the most studied areas.
And the heart? Three or four cups often appear in studies
In 2017, a huge umbrella review published in the BMJ reviewed more than 200 meta-analyses of observational studies. Overall, coffee consumption was more often associated with benefits than harm and, for several parameters – including general and cardiovascular mortality – the statistically most favorable associations often appeared around three or four cups per day.
It’s very easy to turn that number into the “ideal amount of coffee.” It’s not. The same authors underlined the need for robust clinical studies to understand how much of these associations is really caused by coffee. Furthermore, an American “cup”, an Italian espresso and a coffee prepared with the French press do not contain the same amount of caffeine at all.
How we prepare the coffee also matters
It’s not just the taste that changes. The brewing method also changes what ends up in the cup. Unfiltered coffee contains higher amounts of cafestol and kahweol, two diterpenes that can increase LDL cholesterol. Paper filters manage to retain a large part of it, while preparations such as boiled, Turkish or French press coffee let larger quantities pass through.
This doesn’t automatically make one type of coffee “bad” and the other “good”, but it is one of those details that get lost when we talk about coffee as if it were always the same drink. The bean, the roasting, the grinding, the quantity of water, the preparation and of course what we add to it change. A black coffee and a large glass with syrups, cream and a lot of sugar above all share the name.
How much coffee can we drink?
For healthy adults, EFSA generally considers a total intake of up to 400 milligrams of caffeine per day, spread throughout the day, to be safe. For pregnant women the indicated limit drops to 200 milligrams per day, considering all sources of caffeine. But 400 milligrams is not a goal to reach.
Anxiety, palpitations, insomnia, reflux and intestinal disorders can appear much earlier in those who are particularly sensitive. And those who take certain medications should evaluate any interactions with their doctor.
Perhaps the most useful data is less spectacular than the headlines about “coffee that extends life”: our daily cup is a chemically much more complex mixture than caffeine alone. It interacts with the brain, gut, and metabolism, and some of these interactions appear to exist even when caffeine is removed. In short, for once, decaffeinated coffee can stop being treated like the sad cousin of real coffee.
