A variety of approaches have been studied to overcome the problems encountered with using antibiotics, which are ineffective in treating Helicobacter pylori infections. In our study, chitosan/poly-gamma-glutamic acid nanoparticles incorporated into pH-sensitive hydrogels were developed as an efficient carrier for amoxicillin delivery. Our results indicate that hydrogels are pH-sensitive, leading to protecting nanoparticles from being destructed by gastric acid. The results of drug releasing in vitro study clearly indicate that the amount of amoxicillin released from nanoparticles incorporated in hydrogels at pH 1.2 was relatively low (14%), compared to that from only nanoparticles (50%). Confocal laser scanning microscopy revealed that nanoparticles could infiltrate cell-cell junctions and interact with H. pylori infection sites in the intercellular spaces. Additionally, the incorporation of amoxicillin-loaded nanoparticles in a hydrogel protected the drug from the actions of the gastric juice and facilitated amoxicillin interaction specifically with intercellular spaces, the site of H. pylori infection.