Bioceramic cements have been widely used in endodontic treatment. This study aimed to compare the microhardness, elastic modulus, internal microstructure and chemical compositions of Biodentine, WMTA, ERRM Putty, iRoot FS and IRM after exposure to PBS, butyric acid, and butyric acid followed by PBS.Specimens of each material were prepared and randomly divided into 5 subgroups (n = 5): subgroup A: PBS (pH = 7.4) for 4 days, subgroup B: PBS (pH = 7.4) for 14 days, subgroup C: butyric acid (pH = 5.4) for 4 days, subgroup D: butyric acid (pH = 5.4) for 14 days, subgroup E: butyric acid for 4 days followed by 10 days in contact with PBS. The surface microhardness, elastic modulus, internal morphologic and chemical compositions of specimens were analyzed.The microhardness and elastic modulus values of all materials were significantly higher in the presence of PBS compared to exposure to butyric acid, with the same setting time (P < 0.01). After 4-day exposure to butyric acid followed by 10-day exposure to PBS, the microhardness values returned to the same level as 4-day exposure to PBS (P > 0.05). Biodentine showed significantly higher microhardness and elastic modulus values than other materials, while IRM displayed the lowest (P < 0.01).Biodentine seems the most suitable bioceramic cements when applied to an infected area with acidic pH. Further storage at neutral pH, e.g. PBS reverses the adverse effects on bioceramic cements caused by a low pH environment.© 2023. BioMed Central Ltd., part of Springer Nature.