Introduction: Silver diamine fluoride (SDF) is employed as an adjunct cariostatic agent in the management of dental caries in high-risk population. Other than fluorides, chlorhexidine (CHX) is the most potent antimicrobial and efficacious agent against Streptococcus mutans. Aim: The aim of this study is to evaluate and differentiate the efficacy of 38% silver diamine fluoride, CHX varnish, and fluoride varnish on carious primary teeth. Materials and Methods: Ninety children having a count of ≥1 carious lesion were recruited. Thirty-eighty percent silver diamine fluoride or fluoride varnish and CHX varnish were topically applied on the lesion. The primary outcome measured was the arrest of carious lesion (lesion rendered inactive as per the Nyvad criteria) after a follow-up of 14–21 days. Dental biofilm sample was obtained from each child and subsequently assessed for microbial composition by colony-forming unit method before and after treatment followed by protein analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis method. Results: Average proportion of arrested caries lesions in the SDF group was higher followed by CHX and fluoride varnish groups. Decreased total protein amount was found in SDF group. This proves that there is decrease in microbial load posttreatment in SDF group. Conclusion: Thirty-eight percent SDF is more effective than CHX varnish and fluoride varnish in arresting dentin carious lesions in young children.