Coffee is widely appreciated for its ability to increase alertness, largely because of caffeine. Yet caffeine represents only one part of coffee's chemistry.

A single cup contains hundreds of bioactive compounds that can interact with digestion, gut microbes, medications and nutrients.

1. Coffee Can Stimulate Bowel Activity

For some people, coffee can create an urge to have a bowel movement shortly after drinking it. Research discussed in the article found that around three in 10 people report this response. The effect can happen quickly and occurs with both regular and decaffeinated coffee. This indicates that caffeine alone cannot explain the reaction.

The precise coffee compounds responsible have not yet been established. Timing may also play a role. The colon naturally tends to become more active in the morning, which happens to be when many people drink their first cup. What is added to coffee can also influence bowel activity. Lactose from milk and certain sugar-free sweeteners may stimulate the bowels, particularly when consumed in larger quantities.

2. Coffee Can Affect Reflux, Eyes and Ears

Coffee may worsen reflux symptoms in some people. Reflux occurs when stomach acid moves back into the esophagus. The resulting effects are not necessarily limited to heartburn and can include coughing, wheezing and other respiratory symptoms when reflux reaches the throat and airways.

Caffeine can also temporarily raise pressure inside the eye in some people with glaucoma or ocular hypertension. Because pressure may already be elevated in these conditions, controlling it is important for protecting the major nerve responsible for vision. Coffee and caffeine can also be relevant to certain ear symptoms.

3. Coffee Can Interact With Medication

Coffee can change how certain medicines behave in the body. For example, drinking coffee can reduce absorption of levothyroxine, a thyroid medication, as well as alendronate, a medicine used for osteoporosis. The interaction can also occur in the opposite direction. Some medicines can change how caffeine is processed.

Caffeine can slow the metabolism of clozapine, potentially increasing its concentration in the blood. Ciprofloxacin, meanwhile, can slow the breakdown of caffeine, meaning the caffeine from a familiar amount of coffee may remain in the body for longer.

4. Coffee Can Influence Cholesterol

Coffee contains compounds known as diterpenes. Two of them, cafestol and kahweol, can increase total cholesterol and LDL cholesterol. At the same time, short-term research has found that these compounds can lower lipoprotein(a), creating a more complicated picture of coffee's potential relationship with cardiovascular health.

5. Coffee May Interact With Gut Microbes

Coffee does not only interact with the human digestive system. Its compounds can also become available to microorganisms living in the gut. Some chlorogenic acids are not absorbed in the small intestine and instead reach the colon, where gut microbes can break them down into other compounds.

Coffee also contains complex carbohydrates and roasting products called melanoidins. These substances can reach the colon and be fermented by gut microbes. Small human studies suggest that drinking coffee can alter the composition of the gut microbiome.

6. Coffee Can Affect Iron Absorption

Coffee can influence how much iron is absorbed from food. Drinking coffee alongside a meal can substantially reduce absorption of non-heme iron, the form found mainly in plant foods. This effect is not primarily caused by caffeine. Polyphenols in coffee, including chlorogenic acids, can bind with iron inside the digestive tract, making the mineral more difficult to absorb.

7. Coffee Can Activate Digestion

Coffee can stimulate parts of the digestive system even when there is no food waiting to be digested. Both regular and decaffeinated coffee can encourage the pancreas to release trypsin, an enzyme involved in protein digestion. Because decaffeinated coffee produces this response as well, compounds other than caffeine appear to be involved.

Emma Beckett, a senior lecturer in nutrition and food science, explains that coffee should not be viewed simply as a caffeine delivery system. Her article emphasizes the complexity of the beverage and its numerous active compounds: “Coffee is a chemically complicated plant extract containing hundreds of bioactive compounds.”

Coffee's effects extend well beyond increased alertness. Its many compounds can stimulate bowel activity, influence reflux symptoms, interact with certain medications, affect cholesterol-related measurements, interact with gut microbes, reduce absorption of non-heme iron and activate parts of the digestive system. Rather than viewing coffee as simply beneficial or harmful, its effects are better understood as a combination of interactions involving digestion, nutrients, medications and microorganisms in the gut.