Dental caries and oral infections have become a widespread issue in the modern world. This study aimed to investigate the antibacterial, antifungal, and cytotoxicity characteristics of the extracts of Echinacea purpura, Arctium lappa, and the essential oil of Zataria multiflora as a potential herbal mouthwash. The essential oil of Z. multiflora leaves and the extracts of E. purpurea and A. lappa roots were prepared. The characterization was carried out by GC-MS and also, total phenol and flavonoid were assed for all three samples. The antimicrobial and anti-biofilm effects were evaluated against Streptococcus mutans, Streptococcus mitis, Streptococcus salivarius, Lactobacillus acidophilus, Escherichia coli, Staphylococcus aureus, and Candida albicans. The cytotoxic effect of the samples was evaluated on HEK 293 and HDFa cells by MTT test. Thymol and carvacrol contents in EO of Z. multiflora were measured at 31% and 42.2%, respectively. A. lappa had the lowest total phenolic and flavonoid value among the samples. On the other hand, the total phenolic content of Z. multiflora and the total flavonoid content of E. purpurea were the highest. The MIC values of Zataria, Arctium, and Echinacea against S. mutans were 0.011% v/v, 187.5 mg/ml, and 93.75 mg/ml, while MBC were 0.011% v/v, 375 mg/ml, and 187.5 mg/ml, respectively. The formulation showed bactericidal activity against S. mutans in the concentration of 5.86 mg/ml for Echinacea and Burdock extracts and 0.08 µl/ml for EO of Zataria. The formulation significantly affected microbial biofilm formation and induced biofilm degradation. The cell viability percentages were higher than 50% during 24 and 48 h. The formulation had a significant antimicrobial effect on cariogenic bacteria and C. albicans, with the lowest cytotoxic effects. Therefore, this formulation can be an appropriate candidate for mouthwash.