What Coffee Does to Your Body: 7 Surprising Effects

Coffee is famous for caffeine, but a cup contains hundreds of other natural compounds. Research shows these substances can affect digestion, medicines, cholesterol, iron and even the microbes living in the gut.

One of coffee’s quickest effects can happen in the bowel. Some people feel an urge to use the toilet soon after drinking it, and studies show this can happen with both regular and decaf coffee. This suggests caffeine is not the only cause.

Coffee may also worsen acid reflux in some people. Caffeine can temporarily raise pressure inside the eye in certain people with glaucoma or high eye pressure, while its relationship with migraine is complicated because it may either help or trigger headaches depending on the person and amount consumed.

Another important issue is medication. Coffee can reduce the absorption of medicines such as levothyroxine for thyroid disease and alendronate for osteoporosis. Caffeine can also interact with some other drugs, so timing may matter.

How coffee is prepared may influence cholesterol. Coffee contains natural oils called cafestol and kahweol that can raise LDL, or “bad,” cholesterol. Paper filters remove much of these oils, while unfiltered coffee generally contains more.

Coffee also reaches the gut microbes that live in the colon. Some coffee compounds are broken down by these microbes, and small studies suggest regular coffee drinking may change the mix of bacteria in the gut. Scientists are still studying whether these changes are beneficial.

Coffee can also reduce the amount of iron absorbed from a meal, particularly the type of iron found in plant foods. This may matter more for people who already have low iron levels or eat mainly plant-based sources of iron.

Finally, coffee can activate parts of digestion even before food arrives. Both regular and decaf coffee can stimulate digestive activity, showing again that coffee’s effects extend beyond caffeine.

The research discussed across studies published in journals including Nutrients, The American Journal of Clinical Nutrition and other medical and nutrition publications shows that coffee is a complex drink rather than simply a caffeine delivery system.

The evidence is strongest for some effects, such as reduced iron absorption and certain drug interactions, while research on gut microbes and other possible benefits remains less certain. For most people, the practical message is that the amount, preparation method, timing and individual health conditions can all change how coffee affects the body.