Background: To evaluate tooth discoloration by newly developed calcium silicate-based materials, and to examine the pre-application of dentin bonding agent (DBA) for preventing discoloration caused by mineral trioxide aggregate (MTA). Methods: The roots of 50 premolars were randomly divided into five groups (n = 10) and cavities were prepared from resected root surfaces. MTA was placed in the cavities of teeth belonging to the ProRoot MTA (MTA) and RetroMTA (RMTA) groups. For teeth belonging to the ProRoot + DBA (MTA-B) and RetroMTA + DBA (RMTA-B) groups, DBA was first applied to the cavities prior to the addition of MTA. Teeth in the control group were restored with composite resin only (i.e., without MTA). After 12 weeks, MTA was removed from the MTA and RMTA groups and bleaching agents were applied for 3 additional weeks. Color assessments were recorded at baseline, and 1, 4, and 12 weeks, as well as after bleaching. A one-way ANOVA was performed to assess the differences between the two types of MTAs and color changes following DBA pre-application in each MTA group. A p-value of < 0.05 was considered indicative of statistical significance. Results: Following 12 weeks of MTA treatment, there was a significant difference between the discoloration in the MTA and RMTA groups (p < 0.05). However, no significant difference was observed between the RMTA and RMTA-B groups (p > 0.05). Following bleaching, the color changes (ΔE values) of the MTA group were not significantly different from those of the MTA-B group (p > 0.05). The difference of ΔE between the RMTA group after internal bleaching and the RMTA-B group was also not significant (p > 0.05). Conclusions: RetroMTA caused significantly less discoloration than ProRoot MTA. Pre-application of DBA reduced discoloration caused by ProRoot MTA. MTA discoloration was improved equally well between DBA pre-application and post-bleaching.