Introduction: Dental caries is a significant global public health concern in children. Streptococcus mutans (S. mutans) has a significant role in the initiation and progression of dental caries. In Ayurveda, many plants are utilized to prevent caries. Licorice (mulethi), also known as Glycyrrhiza glabra and triphala are the major elements in Ayurveda with several medicinal properties. Triphala extract efficiently reduces the development of plaque on the tooth surface. Lollipops have the ability to self-clean and are effective saliva stimulators. Therefore, the objective of the current study was to evaluate the antibacterial efficacy of licorice and triphala lollipops against S. mutans. Aim: To compare and evaluate the antimicrobial efficacy of licorice and triphala lollipops on S. mutans count in children aged 4–8 years. Materials and methods: A total of three groups were made group I triphala, group II licorice, and group III placebo (sugar-free) lollipops. Children were screened at the baseline, and those who met the inclusion criteria were enrolled in the research after their parents submitted informed consent. Saliva samples were obtained in the early morning on an empty stomach. Then each child was offered a lollipop and saliva samples were carried out on all the follow-up days, that is, 7, 14, and 21. The palatability of lollipops among children was assessed by using a 5-point Likert scale. Results: By using multiple comparisons—Tukey's test, statistically significant difference was found between the triphala lollipop and licorice group (p = 0.0001), the triphala lollipop and placebo group (p = 0.0001), and between the licorice lollipop and placebo group (p = 0.0001) against S. mutans count. Conclusion: Both licorice and triphala lollipops had an antimicrobial effect on S. mutans count. Licorice lollipops had an enhanced antimicrobial effect compared to triphala lollipops.