Why it can affect you: Last (and certainly least) is the beloved, dark, any-time-of-day treat. While chocolate has been proven to have health benefits, including improved cardiovascular health and reduced risk of stroke, it can also cause indigestion and heartburn. "Chocolate contains concentrations of theobromine, a compound that occurs naturally in many plants such as cocoa, tea and coffee plants," stated Lamm. "And this compound has the ability to relax the esophageal sphincter muscle, letting stomach acid squirt up into the esophagus." Chocolate also contains caffeine, another agent that encourages the stomach to produce excess acid.