Background/introduction: Cavity disinfection before restoration aids in reducing the number of residual bacteria, thus, decreasing the rate of secondary caries. Propolis, at low concentrations, inhibits the growth of cariogenic bacteria. Liquorice roots are known to have antimicrobial, anti-inflammatory, and antioxidant properties. Aim and objectives: Evaluation and comparison of antimicrobial efficacy of liquorice and propolis extract gels used as cavity cleaning agents against Streptococcus mutans in deciduous molars by confocal laser scanning microscopy (in vitro study). Materials and methods: Liquorice and propolis extracts were converted into gels after recording the minimum inhibition concentration. Class I cavity was prepared on 135 extracted deciduous molars and subjected to inoculation with S. mutans. Teeth were randomly divided into groups I, II, and III which were treated with gels of liquorice, propolis, and distilled water, respectively, for 60, 120, and 180 seconds each. Specimens were sectioned and stained with fluorescent dyes and observed under a confocal laser scanning microscopy (CLSM). The data obtained were statistically evaluated. Results: The mean nonviable/viable bacterial count and the depth of penetration were found to be maximum in group I and minimum in group III. A statistically significant difference was found to be between groups I and II and groups I and III, while with groups II and III, it was nonsignificant at all 60, 120, and 180 seconds. The bacterial depth penetration between groups I and II at 180 seconds was nonsignificant. Conclusion and clinical significance: Though liquorice showed better antimicrobial potential as compared to propolis extract, both can be used efficiently as cavity disinfectants.