Enamel demineralization is a common problem found in patients using orthodontic devices, such as orthodontic braces. It was found that Streptoccocus mutans growth increases adjacent to orthodontic devices, which may result in caries development. Incorporated antibacterial quaternary ammonium polyethylenimine (QPEI) nanoparticles were previously shown to be highly efficacious against various bacteria. Combining antibacterial materials in orthodontic cement may be advantageous to prevent bacterial outgrowth adjacent to orthodontic brackets. The aim was to evaluate the efficiency of orthodontic cement containing QPEI nanoparticles in reducing S. mutans and Lactobacillus casei outgrowth adjacent to orthodontic brackets. Orthodontic brackets were bonded to the buccal surfaces of extracted lower incisors. The antibacterial effect on S. mutans and L. casei outgrowth of Neobond bracket adhesive orthodontic cement with and without QPEI nanoparticles was compared. The antibacterial effect was evaluated using crystal violet staining and bacterial count (CFU/mL). The teeth in the experimental group, with the QPEI nanoparticles cement, showed significantly lower optical density (OD) values and CFU counts of S. mutans and L. casei than the teeth in the control group (p < 0.05). Based on the results, it can be concluded that orthodontic cement containing QPEI nanoparticles significantly inhibits S. mutans and L. casei growth around orthodontic brackets.