Treating dentin surfaces with antibacterial agents prior to bonding bioactive restorations might affect their mechanical properties. In this study, we evaluated the effect of silver diamine fluoride (SDF) and chlorhexidine (CHX) on the shear bond strength (SBS) of bioactive restorative materials. Dentin discs were treated with SDF for 60 s or CHX for 20 s and bonded with four restorative materials, namely Activa Bioactive Restorative (AB), Beautifil II (BF), Fuji II LC (FJ), and Surefil One (SO). Control discs were bonded without treatment (n = 10). SBS was determined using a universal testing machine, and a scanning electron microscope (SEM) was used for the evaluation of the failure mode and the cross-sectional examination of adhesive interfaces. The SBS of each material between different treatments and of the different materials within each treatment were compared via a Kruskal–Wallis test. The SBS of AB and BF was significantly higher than that of FJ and SO in the control and CHX groups (p < 0.01). In the latter, SBS was higher in FJ than SO (p < 0.01). SO had a higher value with SDF compared to CHX (p = 0.01). The SBS of SDF-treated FJ was higher than that of the control (p < 0.01). SEM showed a more homogenous and improved interface of FJ and SO with SDF. Neither CHX nor SDF compromised the dentin bonding of bioactive restorative materials.