The purpose of the present study was to evaluate the physicochemical properties and antibacterial activity of three calcium silicate cements. Mineral trioxide aggregate (MTA Biorep “BR”), Biodentine (BD) and Well-Root PT (WR) materials were investigated using scanning electron microscopy (SEM) at 24, 72 and 168 h of immersion in phosphate buffered saline (PBS). The antibacterial activity against Enterococcus faecalis (E. faecalis), the solubility, roughness, pH changes and water contact angle were also analyzed. All results were statistically analyzed using a one-way analysis of variance test. Statistically significant lower pH was detected for BD than WR and BR (p < 0.05). No statistical difference was found among the three materials for the efficacy of kill against E. faecalis (p > 0.05). Good antibacterial activity was observed (kill 50% of bacteria) after 24 h of contact. The wettability and the roughness of BR were higher than for the other cements (p < 0.05). BD was more soluble than WR and BR (p < 0.05). In conclusion, the use of bioceramic cements as retrograde materials may play an important role in controlling bacterial growth and in the development of calcium phosphate surface layer to support healing. Moreover, the premixed cement was easier to use than powder−liquid cement.