Bloating has been reported as a side effect of regular pantoprazole use. One study reported bloating in 43% of patients taking a similar proton pump inhibitor to pantoprazole (called esomeprazole) after 8 weeks. By 6 months, over 50% reporting bloating. Other similar side effects reported with pantoprazole that also can have bloating as a side effect include flatulence, abdominal pain, and diarrhea. Symptoms of bloating include tightness, fullness, or swelling of your stomach area.

Bloating is not commonly reported as a side effect of short-term pantoprazole use. But because pantoprazole decreases acid secretion, it can affect the digestive process and the breakdown of food and cause bloating. Some research suggests untreated Helicobacter pylori may flare up during pantoprazole treatment which may be responsible for bloating with pantoprazole.