Background: Caries excavation is a noninvasive technique of caries removal with maximum preservation of healthy tooth structure. Aim: To compare the efficacy of three different caries excavation techniques in reducing the count of cariogenic flora. Materials and methods: Sixty healthy primary molars were selected from 26 healthy children with occlusal carious lesions without pulpal involvement and divided into three groups in which caries excavation was done with the help of (1) carbide bur; (2) polymer bur using slow-speed handpiece; and (3) ultrasonic tip with ultrasonic machine. Samples were collected before and after caries excavation for microbiological analysis with the help of sterile sharp spoon excavator. Samples were inoculated on blood agar plate and incubated at 37°C for 48 hours. After bacterial cultivation, the bacterial count of Streptococcus mutans was obtained. Statistical analysis: All statistical analysis was performed using SPSS 13 statistical software version. Kruskal-Wallis analysis of variance, Wilcoxon matched pairs test, and Z test were performed to reveal the statistical significance. Results: The decrease in bacterial count of S. mutans before and after caries excavation was significant (p < 0.001) in all the three groups. Conclusion: Carbide bur showed most efficient reduction in cariogenic flora, while ultrasonic tip showed almost comparable results, while polymer bur showed least reduction in cariogenic flora after caries excavation.