Seven ways your coffee habit could be ruining your health, from digestion to cholesterol

Many of us can't start the day without caffeine, but it's important to know coffee can have its downsides too. Photo / Getty Images

Your daily caffeine hit may be doing more harm than good – but there are steps you can take to fix it.

Whether it’s a flat white or a double-shot espresso, many of us can’t start the day without caffeine. A morning cup perks us up after a bad night’s sleep, fuels our workdays and workouts, and powers our social lives. Coffee is also rich in antioxidants, proven to protect us from heart disease and cancer.

But before you reach for a refill, it’s worth knowing that coffee has its downsides, too. Beyond the jitters and sleepless nights, caffeine – and other plant compounds in coffee – can affect everything from digestion and vitamin absorption to cholesterol, mood and stress.

“Coffee has some surprising effects on our gut and overall health,” says Katie Sanders, a specialist gastroenterology dietitian at healthcare provider Doctify. “Like most things in nutrition, it’s not a one-size-fits-all story.”

Here’s what you need to know, to ensure your coffee habit keeps you healthy.

1. It can spike your cortisol

“Caffeine stimulates the sympathetic nervous system – your body’s ‘fight or flight’ response – releasing cortisol and adrenaline,” says Dr Anna Symonds, a chartered clinical psychologist. “It mimics a stress response, raising heart rate, blood pressure and alertness. It also blocks adenosine, which normally promotes calm and sleepiness.”

While coffee boosts dopamine, creating a temporary high, Symonds explains that “if you drink it when you’re anxious, or when cortisol is at its natural peak – around 7am to 8am – you’re essentially double-layering the stress response”. This can result in restlessness, jitteriness and racing thoughts.

Genetics matter too. According to meta-analysis in Frontiers in Psychology, caffeine is metabolised in the liver and your genes influence whether you are a “fast” or “slow” metaboliser. Fast metabolisers can break down caffeine more rapidly and tolerate higher levels without feeling anxious or jittery. Slow metabolisers are more likely to experience side effects, such as anxiety or palpitations, even after a single cup of coffee.

How to fix cortisol spikes

Avoid drinking coffee on an empty stomach; ideally wait 60 to 90 minutes after waking. As cortisol levels are starting to dip, caffeine will give you a better boost without interfering with your body’s rhythms. Stick to one to two cups a day (up to 200mg caffeine). Cut back your intake gradually to avoid withdrawal, and switch to decaf if you want to keep the ritual.

2. It knocks out your deep sleep

A study in Communications Biology, found that people given 200mg caffeine (about two cups of coffee) a few hours before bed, had fewer delta brain waves, linked to deep sleep, and more beta waves, associated with wakefulness. Caffeine also pushed the brain into a state of “criticality” – heightened awareness – potentially disrupting recovery.

“After caffeine, the deeper stages of sleep tend to be shorter, less frequent, and sometimes delayed,” says Dr Allie Hare, a consultant in sleep medicine, the president of the British Sleep Society and co-founder of Grace Sleep. “Deep sleep is vital for removing waste products from the brain, for tissue growth and repair. Chronically reduced deep sleep can increase dementia risk.”

Caffeine’s half-life is five to six hours, meaning half the caffeine from a 4pm coffee can still be in your system at 10pm. This is why late cups of coffee often disrupt sleep.

How to fix insomnia

Both timing and dose of caffeine matter. “Latest research suggests a 100mg dose of caffeine (around one cup) up to four hours before bed, is usually fine,” says Dr Hare. “But 400mg within 12 hours can significantly alter sleep architecture.” Ideally, stop drinking coffee at lunchtime, then adjust timing and intake, according to how your sleep responds, she advises.

3. It can ramp up your cholesterol

Coffee contains natural compounds called diterpenes, linked to higher LDL cholesterol – the “bad” type that clogs arteries – and some brewing methods give you more than others.

“Unfiltered coffee, such as espresso, is high in diterpenes, particularly cafestol and kahweol, which interfere with proteins that transport LDL [bad] cholesterol out of the bloodstream,” says Dr Sam Firoozi, a consultant interventional cardiologist at HCA Healthcare UK. “As a result, LDL levels rise.”

How to manage your cholesterol

“For most people, one or two coffees a day is fine,” says Firoozi. “But if you have risk factors for heart disease, such as diabetes, high cholesterol or smoking, unfiltered coffee could add to your risk. Filtered or instant are safer choices.”

According to research in Nutrition, Metabolism and Cardiovascular Diseases, Turkish-style boiled coffee contains the most diterpenes, followed by some machine brews and espresso. Filter and instant coffee contain very little, as filtering removes the compounds.

4. It may block vitamin absorption

“Some studies suggest even one cup with an iron-rich meal can reduce absorption by 30 to 40 per cent,” says Bini Suresh, the lead for nutrition and dietetics and therapy services at Cleveland Clinic London. “It’s most relevant for those at risk of iron deficiency, like vegetarians.”

As a mild diuretic, caffeine also increases urinary losses of water-soluble nutrients and minerals, including B vitamins, vitamin C, calcium and magnesium. “It’s unlikely to be a problem, unless your coffee intake is very high (more than four cups a day) and your diet is already low in these minerals,” says Suresh.

How to improve vitamin absorption

Avoid coffee around mealtimes, particularly iron-rich meals like beef stir-fry or lentil soup. “Wait at least an hour before or after meals or supplements,” says Suresh. “Pair iron-rich foods with those rich in vitamin C to boost absorption, and limit coffee to under four cups a day.”

5. It disrupts your digestion

“Coffee doesn’t just wake up the brain – it wakes up your gut too,” says Sanders. “Caffeine stimulates digestive hormones, speeding things along in the colon. It’s why so many people get that familiar urge to head to the loo after their first coffee.”

Another compound in coffee, chlorogenic acid, triggers the “gastrocolic reflex” – a wave of movement that propels food through the gut. If you’re prone to digestive issues, this can set off symptoms.

“People with IBS often find coffee worsens cramps, urgency or diarrhoea, and it can aggravate inflammatory bowel disorder,” says Sanders.

Coffee can also worsen heartburn. Caffeine stimulates stomach acid and relaxes the valve at the top of the stomach, increasing your risk of reflux.

How to avoid an upset stomach

If reflux or cramps are an issue, avoid drinking coffee on an empty stomach. “Try a smaller size or cold brew, which tends to be less acidic and better tolerated,” says Suresh. “If symptoms flare consistently, reduce your intake or switch to decaf to see if caffeine is the trigger.”

6. It messes with your medication

“Caffeine can interact with many medicines,” says pharmacist Deborah Grayson, a specialist in drug-nutrient interaction. “It can amplify or counteract a drug’s action, or alter how it’s processed in the liver, leading to higher levels and increased risk of side effects.”

High caffeine intake may impair blood-thinners, like warfarin, by reducing platelets’ ability to clot, says Grayson. And drinking coffee within an hour of taking thyroid medication, levothyroxine, can reduce its absorption by half.

Take care with over-the-counter remedies too. Cold and flu remedies often contain stimulants such as pseudoephedrine, which raise heart rate and blood pressure and may disrupt sleep. “Caffeine can amplify these effects, so it should be used sparingly or avoided,” says Grayson.

Caffeine is added to many painkillers to increase their effectiveness, and drinking coffee may ramp them up further. “However, for some people, the extra caffeine may increase risk of gastritis or stomach bleeds, and also increase the risk of heartburn and indigestion,” says Grayson. “This risk is highest with aspirin, though it can also occur with paracetamol.”

How to make sure your medication isn’t affected

“For most people, one or two coffees a day is safe with common medications,” says Grayson. “But keep a one-to-two-hour gap between taking them and drinking coffee and consult your GP or pharmacist if you’re unsure.”

7. It exposes you to microplastics

A study by researchers at the University of Birmingham found takeaway coffee from high-street chains contains substantial levels of microplastics – tiny fragments of plastic, shed from packaging, that can accumulate in the body and may harm health.

Scientists at the University of Birmingham tested 155 hot and cold popular drinks, from supermarkets and cafes. Coffee ranked second highest (after tea) at 43 microplastic particles (MPs) per litre. The main source? Single-use cups.

How to avoid microplastics

“If you’re grabbing coffee on the go, take a reusable cup,” says Erica Cirino at the Plastic Pollution Coalition. “Choose stainless steel, ceramic or glass, and avoid plastic lids. At home, use ceramic or stainless-steel equipment and recycled-paper filters.”

The UK NHS recommends adults stick below 400mg of caffeine a day. For pregnant women, it’s below 200mg a day. Caffeine levels vary widely according to the size and blend of your coffee. Here’s a quick guide from dietitian Bini Suresh.

How to cut down (without feeling deprived)

By Katie Sanders, a specialist gastroenterology dietitian

“If you’re drinking more coffee than feels good for your gut, sleep, or stress levels, the trick is to cut down gradually,” says Sanders. Here are her tried-and-tested strategies:

Wait a bit

Delay your first cup until mid-morning, after your natural cortisol peaks. It can take the edge off that “I need coffee to function” feeling.

Eat before you drink

A protein-rich breakfast, such as eggs or Greek yogurt, helps steady your energy, reducing the crash that drives you to another cup.

Go half-caf

Mix regular and decaf beans. Ask for a split shot in cafes or alternate between the two during the day.

Reduce the serving

Swap a large mug of coffee for a smaller one. The ritual stays, the caffeine load drops.

Switch it up

Try peppermint or ginger tea, or a brisk walk outdoors instead of that extra afternoon coffee.