Purpose: This study aimed to evaluate and compare the remineralizing and antimicrobial effect of chitosan-based agent and Flavonoid. Materials and methods: This study was carried out in two phases; remineralization phase and antimicrobial phase. Ninety (90) bovine mandibular incisors were used in the study with forty-five (45) teeth in each phase. Teeth were prepared and randomized into three groups according to treatment material (n=15 samples) as follows; group I; control group (being immersed in artificial saliva), group II; treated with flavonoid and finally group III; treated with chitosan-based agent. Each agent was applied for 10 minutes six times/day. In phase (1) remineralizing effect was measured through recording radiodenisty (by using digital radiography) at baseline, after creation of lesion and after treatment. In phase (2) antimicrobial effect was measured (by using colony forming unit test and lactic acid production test) at baseline and after treatment. Data were obtained and the differences between groups were estimated by ANOVA test followed by Tukey's post hoc test. Results: Statistical analysis by ANOVA test revealed that there was high statistically significant difference between the study groups. Dentin blocks treated by chitosan-based agent showed greater remineralizing effect than flavonoid. Dentin blocks with 1,4 and 7 days biofilms treated with Flavonoids showed greater inhibition of Lactic acid production and Colony forming unit. Conclusion:- Chitosan-based agent can be used as remineralizing agent while flavonoid can be used as antimicrobial agent against S.mutans by inhibiting colony forming unit and lactic acid production.