Introduction: Endodontics in primary teeth has brought a revolution in preserving the primary teeth until it is physiological exfoliation. However, reinfection and failure of the pulpectomy-treated teeth should not be neglected. This raises the need for the best root canal filling material with the strongest antibacterial capabilities for primary teeth. The current study set out to assess the antimicrobial efficacy of different concentrations of the novel obturating material against Streptococcus mutans and Enterococcus faecalis, the two most common microorganisms found in primary tooth infections. Materials and methods: The antimicrobial efficacy of the novel obturating material was evaluated against Streptococcus mutans and Enterococcus faecalis using Mueller–Hinton agar (MHA) for 24 hours at 37°C. Twelve distinct concentrations of the material were prepared by varying the proportions of calcium hydroxide, zinc oxide, and metronidazole. After a day, the zone of inhibition was measured in millimeters. After entering the input into a Microsoft Excel spreadsheet, the values underwent statistical analysis. Results: The mean zone of inhibition against Streptococcus mutans and Enterococcus faecalis was greater with 2% 60–40 concentration of the novel obturating material. However, no statistically significant difference was noted (p = 0.74, 0.22, respectively). Conclusion: The most effective formulation of the novel obturating material with the greatest antimicrobial property was determined to be 2% 60–40 concentration of metronidazole, calcium hydroxide, and zinc oxide.