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Background: The oral microflora primarily involved in early childhood caries (ECC) is Streptococcus mutans while Streptococcus sanguinis is related to healthy caries‑free mouth. The antagonism between the two at biological level is well recognized. Aim: This study aims to compare the pre‑ and posttreatment salivary levels of S. mutans and S. sanguinis in ECC. Methods: This cross‑sectional study was performed on 40 eligible participants. Clinical examination was done, and decayed teeth were recorded. Pre‑ and Posttreatment saliva sample was taken, processed and bacterial counts were compared. Results: A statistically significant posttreatment reduction was found in S. mutans counts; however, a significant posttreatment elevation was seen in S. sanguinis counts (P < 0.001) using Wilcoxon signed‑rank test. A significant weak positive correlation was found between S. mutans and decayed teeth in the mouth (r = 0.366 and P = 0.028) using Spearman’s correlation. No significant gender association was found between pre‑ and posttreatment S. mutans and S. sanguinis counts (P = 0.908) and also between decayed teeth (P = 0.321) using Mann–Whitney U‑test. Conclusion: Complete dental treatment procedure showed significant reduction and elevation in S. mutans and S. sanguinis counts, respectively. A positive association was observed between S. mutans and ECC while S. sanguinis were positively associated with posttreatment oral environment.