Peptic Ulcer Disease. Chocolate may cause you stomach pain if you have a hole in the lining of your stomach or small intestine called a peptic ulcer. With treatment, ulcers heal in several months, so you should be able to enjoy chocolate again, according to MedlinePlus.eartburn and GERD. Chocolate is a common trigger for gastroesophageal reflux disease, a more serious condition related to heartburn. GERD occurs when the sphincter between the stomach and esophagus does not seal tightly, allowing stomach acid to wash back into the esophagus.