This In Vitro study investigated the effects of incorporating copper nanoparticles (CuNPs) into an etch-and-rinse (ER) adhesive on the survival rate of Streptococcus mutans (S. mutans), micro tensile bond strength (μTBS), and degree of conversion (DC) when applied to carious dentin. Mandibular teeth with carious lesions were selected, and S. mutans was inoculated on carious-affected dentin (CAD). The samples were divided into four groups based on the concentration of CuNPs in the OptiBond FL primer: Group 1 had unmodified ER adhesive, Group 2 had 0.1 wt% CuNPs, Group 3 had 0.5 wt% CuNPs, and Group 4 had 1 wt% CuNPs. The survival rate of S. mutans was assessed, and the samples were restored to evaluate μTBS and failure modes. The DC was measured using Fourier Transform Infrared Spectroscopy (FTIR). Statistical analysis using ANOVA and Tukey tests determined significant differences across groups in antibacterial efficacy, μTBS, and DC. The results indicated that the 1 wt% CuNPs group (Group 4) exhibited the lowest bacterial survival, while the unmodified ER adhesive group (Group 1) showed the highest S. mutans survival. The highest bond strength to the CAD was observed in the 0.5 wt% CuNPs group (Group 3), with Group 1 demonstrating the lowest μTBS. These findings suggest that incorporating CuNPs into an ER adhesive system, particularly at a concentration of 0.1 wt%, can effectively provide antimicrobial properties to the adhesive interface while simultaneously enhancing bond strength and achieving a favorable degree of conversion with carious-affected substrates.