Aim: Compare the efficacy of triple antibiotic paste (TAP), herbal extracts, and camphorated monochlorophenol (CMCP) as intracanal medicaments against Enterococcus faecalis (E. faecalis) in deciduous molars. Materials and methods: A total of 60 samples were collected from canals of first and second molars of 4–10-year-old children, with more than two-thirds root length, and fitting the inclusion criteria. Samples were collected at three intervals—S1 was collected just after access opening, S2 was collected after biomechanical preparation (BMP) and irrigation, and just before placement of medicament. Randomization was done to place the medicaments into three groups: group I—CMCP, group II—TAP, and group III—herbal combination. Sample S3 was taken 48 hours after removal of medicament from the canals. The collected samples were transported via Amies media to the laboratory, where they were anaerobically incubated for 24 hours. Growth of E. Faecalis was observed, and manual counting of the colony-forming unit (CFU) was done. The change in CFU in all samples was calculated, and the results were statistically analyzed. Results: The results show that there is a change from S1 (TAP = 118.67 ± 122.48, herbal = 109.07 ± 106.43; CMCP = 110.73 ± 120.53) to S2 (TAP = 34.13 ± 63.47; herbal = 27.67 ± 39.39; CMCP = 16.40 ± 26.32) and S3 (TAP = 12.33 ± 24.82; herbal = 4.73 ± 12.78; CMCP = 3.40 ± 7.12). It is seen that there is a significant difference seen from S1 to S2 in all three groups (p ≤ 0.05) using repeated measure analysis of variance (ANOVA) test. This shows that all three medicaments were effective in reducing bacterial counts of E. Faecalis from sample S1 (pre) to S3 (post) significantly after exposure to root canal bacterial flora for 48 hours (2 days). The pairwise comparison of the change in CFU within each group, S1–S3, also shows significant changes. There is a significant decrease in CFU seen from S1 to S2 and S1 to S3 but not from S2 to S3 for all three groups, which was evaluated using the post hoc Bonferroni test. It was also observed that in between the canals, although there was a change from S1 to S3 in terms of the CFU, there was no significant difference in the decrease in the bacterial count when intercanal comparison was made. There was, however, a change that was seen to be significant when values from each canal were compared from S1 to S3. Conclusion: All three medicaments have successfully shown a decrease in the numbers of E. faecalis, which the study aimed at checking. Although the effect varied intergroups, it was mild, so herbal alternatives could be used instead of antibiotics and CMCP. Also, because the local application is effective in controlling interappointment flare-ups, the medicaments can be successfully given without having to prescribe systemic antibiotics.