Aims: Zirconium oxide (ZrO2) and Titanium dioxide (TiO2) nanoparticles (NPs) in-cooperated in a three-step etch and rinse adhesive against Lactobacillus survival rate, shear bond strength (SBS) and marginal leakage on CAD. Methods: Ninety premolars having occlusal carries to the middle third of the dentin were included. Inoculation of Lactobacillus on CAD surface was performed on 30 samples. The remaining 60 samples were then divided into three groups based on primer applied in three steps etch and rinse (n = 20) Group 1 (Optibond FL), Group 2: (Optibond FL + TiO2), and Group 3: (Optibond FL + ZrO2). The survival rate was assessed on the 30 samples. The remaining 60 samples were applied with Optibond FL bonding agent and composite restorative material. Microleakage, SBS, and failure mode were analyzed. The means and standard deviations (SD) were compared utilizing ANOVA followed by a post hoc Tukey multiple comparison test. Results: Specimens in Group 1 demonstrated the maximum numbers of Lactobacillus species and marginal leakage values. Group 2 specimens displayed the minimum count of bacteria, lowest microleakage scores, and highest bond values. However, Group 1 specimens showed the lowest bond integrity. Conclusions: ZrO2 and TiO2 NPs filled dental adhesive demonstrated better antimicrobial efficacy and bond strength. They also cause a reduction in marginal leakage at the resin dentin interface.