Incorporation of cross-linked quaternary ammonium polyethylenimine (QPEI) nanoparticles in dental resin composite has a long-lasting and wide antimicrobial effect with no measured impact on biocompatibility in vitro. We hypothesized that QPEI nanoparticles incorporated into a resin composite have a potent antibacterial effect in vivo and that this stress condition triggers a suicide module in the bacterial biofilm. Ten volunteers wore a removable acrylic appliance, in which two control resin composite specimens and two resin composite specimens incorporating 1% wt/wt QPEI nanoparticles were inserted to allow the buildup of intraoral biofilms. After 4 h, the specimens were removed and tested for bacterial vitality and biofilm thickness, using confocal laser scanning microscopy. The vitality rate in specimens incorporating QPEI was reduced by > 50% (p < 0.00001), whereas biofilm thickness was increased (p < 0.05). The ability of the biofilm supernatant to restore bacterial death was tested in vitro. The in vitro tests showed a 70% decrease in viable bacteria (p < 0.05). Biofilm morphological differences were also observed in the scanning electron microscope micrographs of the resin composite versus the resin composite incorporating QPEI. These results strongly suggest that QPEI nanoparticles incorporated at a low concentration in resin composite exert a significant in vivo antibiofilm activity and exhibit a potent broad spectrum antibacterial activity against salivary bacteria.