INTRODUCTION: Chemomechanical caries removal (CMCR) is an effective method of caries removal especially for primary teeth as they cause less discomfort when compared with conventional caries removal. The most significant thing about caries removal is the elimination of cariogenic bacteria. This study compares the antibacterial activity of two CMCR gels. MATERIALS AND METHODS: A total of 40 primary molar teeth with carious dentin were split along the long axis in a laboratory. Total viable count (TVC) was taken for the teeth before splitting as a measure of colony-forming units per milliliter (CFU/mL). Each half was treated with either Carisolv or Carie-Care CMCR gels. Clean dentin samples were evaluated for Streptococcus mutans (SM) and Lactobacillus acidophilus (LB) after removal of carious tissue using the caries removal gels using serial dilutions and incubating on specific agar plates. RESULTS: The results showed significant reduction in mean TVC after use of both the CMCR gels. Both gels reduced the CFU/mL of SM and LB to a significant level (p < 0.05). However, there was no significant difference between the antibacterial activities of the two CMCR gels. CONCLUSION: The CMCR gels (Carisolv and Carie-Care) significantly reduced the residual TVC as well as SM and LB in carious primary dentin. Both CMCR gels had a similar antibacterial activity on the carious dentin of primary teeth. CLINICAL SIGNIFICANCE: The CMCR gels tested have a significant antibacterial activity and can be effectively used for elimination of caries-causing bacteria in primary teeth.