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.