Early childhood caries (ECC), a severe form of dental caries, is exacerbated by the synergistic interaction between Streptococcus mutans and Candida albicans, leading to greater disease severity than their individual effects. This underscores the need for more targeted and potent therapeutic alternatives. Given the promising anti-infective properties of quaternary ammonium surfactants (QAS), this study explores the microbicidal properties of one such QAS, cetyltrimethylammonium chloride (CTAC), against both individual- and dual-species cultures of S. mutans and C. albicans for effective ECC treatment. Initially, the minimal inhibitory concentrations (MICs) of CTAC were determined to range from 4 to 8 µg/mL against S. mutans, C. albicans, and dual-species cultures. Time-kill kinetics, assessed via spot assays and spectrometry, demonstrated that CTAC completely eradicated both individual- and dual-species cultures within 30 min of exposure. Furthermore, at sub-MIC concentrations, CTAC effectively reduced biofilm formation and virulence traits in S. mutans (including acidogenicity and aciduricity) and C. albicans (including yeast-to-hyphal transition and filamentation). To explore therapeutic application, a mouthwash containing CTAC was formulated. The results showed that the formulated CTAC mouthwash was as effective at eradicating pathogens as a commercially available mouthwash containing 0.075% cetylpyridinium chloride (CPC). Moreover, the CTAC mouthwash maintained stable physicochemical characteristics and antimicrobial activity over 4 weeks. It exhibited rapid killing activity against pathogens, achieving efficacy within just 2 min of exposure. Fluorescence microscopy and SEM micrographs confirmed the strong biofilm eradication potential of the CTAC mouthwash. The non-toxic nature of the formulated mouthwash was validated using human buccal epithelial cells, and in vivo studies further demonstrated that CTAC mouthwash significantly reduced bacterial and fungal loads in Galleria mellonella. Overall, the findings of this study highlight the potential application of QAS-CTAC in the treatment of ECC., Competing Interests: Declarations. Ethical Approval: In the present study, human buccal epithelial cells and saliva samples were used. The collection process adhered to established ethical guidelines and was approved by the Institutional Ethical Committee of Alagappa University, Karaikudi (approval reference: IEC/AU/2018/5). Consent to Participate: Informed consent was obtained from all participants involved in the study. Consent for Publication: Not applicable. Competing Interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)