Periodontal disease comprises a group of inflammatory conditions of periodontal tissues with common etiologic agent (bacteria) in the form of dental plaque. The objective of this research was to prepare a water-in-oil type microemulsion comprising metronidazole and equate its potency towards the effective treatment of periodontitis. A pseudo ternary phase diagram for microemulsion investigated using quaternary system containing water/captex 500/tween 80/acconon CC6. The microemulsion was preferred from the microemulsion area on the phase diagram. Stable water-in-oil type metronidazole microemulsion was prepared successfully using the quaternary system of water/captex 500/tween 80/acconon CC6 at 4:1 ratio having droplet size in the range of $81{pm}12.91$ to $196{pm}10.73nm$, conductivity $50.6{pm}0.8$ to $330.7{pm}1.1{mu}s/cm$. In-vitro drug release, in vitro and ex vivo antimicrobial activities by agar well diffusion were investigated. Metronidazole Microemulsion loaded hydrogel formulations (F9 and F10) were found to be optimized for maximum release and antimicrobial activity in terms of zone of inhibition. The in vitro release evidenced that metronidazole microemulsion loaded hydrogel release rate was maximum as compared to other plain metronidazole gels. Stability study proved that microemulsion persisted stable for at least 6 months; with no changes in clarity, characteristic properties, and no sign of crystallization of metronidazole. In ex vivo evaluation, microemulsion based hydrogels were effective against the microbial flora of the human oral cavity suffering from periodontitis. The system was found to be appropriate for application and more effective in reducing the clinical symptoms of periodontitis.