We aimed to compare the plasma pantoprazole level (PPL) between patients with type 2 diabetes mellitus and non-diabetic patients during Helicobacter pylori (H. pylori) eradication treatment and to explore the role of PPL in predicting the treatment success rates. This study included 40 diabetic and 40 non-diabetic treatment-naive H. pylori-infected patients. Bismuth-based standard quadruple treatment for H. pylori eradication was used for 14 days in both groups. PPL was measured using the square-wave voltammetry method. H. pylori eradication rate (60.0% vs 87.5%, P = 0.005) and PPL (0.25 ± 0.03 μg/mL vs 0.34 ± 0.03 μg/mL, P < 0.001) was significantly lower in the diabetic group compared with the controls. Patients with treatment failure had lower PPL than those with successful treatment (P < 0.001). The receiver operating characteristics curve demonstrated that PPL had a significant predictive value for the outcome of H. pylori eradication. Type 2 diabetic patients had lower PPL than the non-diabetic controls, which led to their lower H. pylori eradication rates.