Aim: To incorporate different concentrations of zirconia/silver phosphate (ZrO2/Ag3PO4) nanoparticles (NPs) in self-etch (SE) adhesive. Surface characterization, elemental analysis, survival rate assessment of S. mutans, micro-tensile bond strength (μTBS), and the degree of conversion (DC) of composite bonded to caries-affected dentin (CAD) were determined. Material and Methods: This study employed a comprehensive methodological approach, incorporating a variety of analytical techniques, including scanning electron microscopy (SEM) combined with energy-dispersive X-ray spectroscopy (EDX), Fourier transform infrared (FTIR) spectroscopy, and μTBS testing. Eighty human third molars that had caries advancement up to the middle third of the dentin were included. Samples were distributed into four groups based on concentration of ZrO2/Ag3PO4 NPs in the primers of the two-step SE adhesive: Group 1 (Control): unmodified SE adhesive; Group 2: 0.15 wt% ZrO2/Ag3PO4 + SE adhesive; Group 3: 0.25 wt% ZrO2/Ag3PO4 + SE adhesive; Group 4: 0.5 wt% ZrO2/Ag3PO4 + SE adhesive. SEM was employed to investigate the morphological characteristics of ZrO2/Ag3PO4 NPs. For elemental distribution EDX spectroscopy and to assess the of cured and uncured adhesive with changed concentrations of NPs, FTIR spectroscopy were performed. Antibacterial efficacy was calculated in adhesives with different concentrations of ZrO2/Ag3PO4 using the pour plate method. For μTBS assessment, a compressive force was applied at the material–dentin interface at a crosshead speed of 0.5 mm/min. The debonding process of each specimen was measured in MegaPascals (MPa). One-way analysis of variance (ANOVA) and Tukey’s post hoc test were used to compare the means and standard deviation (SD) between groups. Results: The samples from Group 4, which were applied with 0.5 wt% ZrO2/Ag3PO4 + SE, displayed the lowest survival rate (0.12 ± 0.01 CFU/mL) of S. mutans. The strongest bond of composite to the CAD surface was observed in Group 4 (0.5 wt% ZrO2/Ag3PO4 + SE) (20.12 ± 0.79 MPa). The highest DC was observed in the control group (unmodified SE (69.85 ± 8.37)). Conclusion: The self-etch adhesive modified with ZrO2/Ag3PO4 nanoparticles showed a favorable effect on micro-tensile bond strength (μTBS) and demonstrated enhanced antibacterial efficacy against S. mutans.