In this study, novel, quaternary ammonium methacrylate–modified silica nanoparticles (QMSNs) were synthesized for the first time and proposed as possible antimicrobial particles for free-radical, photocurable monomers. Such monomers have the potential to polymerize with other methacrylate monomers and create antimicrobial polymers. The silica nanoparticles were modified by quaternary ammonium methacrylate functionality and incorporated at 0 to 10 wt% into a 1:1 (by mass) bisphenol A glycerolate dimethacrylate (BisGMA)/triethylene glycol dimethacrylate (TEGDMA) resin. Thermal stability of the pristine and modified silica nanoparticles was examined by thermogravimetric analyses. Atomic force microscopy was used to investigate the size distribution and topography of the nanoparticles. For evaluation of the mechanical properties of the samples, flexural strength was measured using a 3-point bending test method. The flexural strength of the composites containing QMSNs increased with increasing modified silica content. The antimicrobial activity of samples was investigated against some standard microorganisms (Streptococcus mutans, Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, and Candida albicans), and then cytotoxicity and viability were quantified. Incorporation of 2.5% to 10% (by mass) QMSNs into BisGMA/TEGDMA demonstrated antimicrobial activity, but ≥5 wt% significantly reduced cell viability