Introduction: Medicinal plants have long been of great interest to scientists in the search for the best treatment of diseases, especially the infectious diseases. In recent years, the use of herbal medicines has become more well-known because of their antimicrobial, antifungal, anti-cancer and less side effects. Aim: The aim of this study was to investigate the antimicrobial and antifungal effects of Urtica dioica, Equisetum arvense, and Punica Granatum peel extracts on two common oral microorganisms, Streptococcus mutans and Candida albicans. Materials and methods: The study investigated the hydro-alcoholic extract of the plants. The antimicrobial activity of the extracts was evaluated using the method of measuring the inhibition of microorganisms, and the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) were determined using different concentrations of the extracts and also biofilm assay and SEM were determined. Also cell viability was assessed by MTT assay on human gingival fibroblast cells. Results: The lowest MIC against S. mutants and C. albicans was related to the hydro-alcoholic extract of U. dioica. There was a significant reduction in the microbial biofilms by all three extracts. Among them, U. dioica could decrease the biofilms of S. mutans and C. albicans more than other extracts. In addition, the best results for growth inhibition zone were the hydro-alcoholic extracts of E. arvense and U. dioica with 35 and 30 mm growth zone, respectively. The results of SEM showed that P. granatum peel, U. dioica and E. arvense could destroy microbial biofilms without exerting any cytotoxic effects on HGF cell. Conclusions: The results of the study suggest that U. dioica, E. arvense, and P. Granatum peel extracts can be used as mouthwash with the least significant difference with routine mouthwashes. Also, the plant-based mouthwashes may be more suitable substitutes for chemical types in the future.