The porpoise of the study was to evaluate the antibacterial effect of silver nanoparticles (Ag-NPs) versus chlorhexidine (CHX) against Streptococcus mutans and Lactobacillus casei. Three different reducing agents were used for the synthesis and characterization of Ag-NPs: sodium borohydride (NaBH 4), a chemical method, and Heterotheca inuloides (Hi) and Camellia sinensis (Cs), two eco-friendly methods. The synthesized substance was deposited on deciduous teeth. Its behavior in dental tissues was evaluated through an energy dispersive X-ray spectroscopy (EDS) analysis, using a scanning electron microscope (SEM). The characterization of Ag-NPs in terms of shape, size, and polydispersity was performed through spectrophotometry of ultraviolet-visible light analysis (UV-vis), as well as by transmission electron microscopy. Isolation and culture of strains S. mutans and L. casei were done to perform the microbiological analysis. In Petri dishes, paper discs containing different concentrations of Ag-NPs (synthesized by Hi, and by Cs) were deposited and tested along with paper discs containing CHX. Their antibacterial effect against both bacteria was evaluated by the inhibition zones test. By means of UV-Vis and TEM analysis, it was possible to observe that Heterotheca inuloides produced smaller and more stable nanoparticles, also in greater quantities (17.5 nm), when compared to Camellia sinensis. EDS analysis through SEM showed a 6.25 average absorption of silver in dental tissues. The microbiological analysis revealed a greater zone of inhibition when the test bacteria were in contact with 20 μl of Ag-NPs, synthesized by Hi, being statistically significant (p < 0.05), compared to the growth inhibition zones produced by Cs, and CHX against both strains. We can conclude that eco-friendly methods produced Ag-NPs with an important antibacterial effect in both strains.