AimsThe existing study aimed to assess the survival rate of S.mutans and shear bond strength (SBS) of resin adhesive restoration bonded to carious affected dentin (CAD) after using different cavity disinfectants (Chitosan, Fotoenticine®, and CO2 laser) in comparison to Chlorhexidine (CHX). Materials and methodsThe study included human mandibular molars assessed on International Caries Detection and Assessment System (ICDAS) score 4 and 5. The cusp part of the clinical crown was cut off until the reduction reaches the central fossa while being continuously supplied with water coolant till the tooth cementoenamel junction (CEJ). The root sections were embedded in polymethyl methacrylate acrylic resin followed by culturing S.mutans biofilm on the CAD surface. Specimens were arbitrarily allocated into four groups(n = 10) based on the type of disinfection. Group 1 (2% CHX), Group 2 (Chitosan), Group 3 (Fotoenticine), and Group 4 (CO2 laser). S.mutans survival rate was assessed and CAD was restored with a composite restorative material. Thermoocycling of the samples was performed and a universal testing machine (UTM) and Stereomicroscope were used to identify bond integrity and type of fracture. ANOVA and Tukey multiple comparison tests were used to assess SBS. Data on the survival rate of S. mutans were compared between groups using the nonparametric Kruskal-Wallis test ResultsOutcomes revealed that Group 1 (CHX) displayed the highest survival rate (0.65 ± 0.10). However, lowest survival rate was demonstrated by Group 3 (Fotoenticine) treated specimens (0.25 ± 0.06). It was also discovered that CHX unveiled highest bond strength values (21.48 ± 1.39 MPa). Nevertheless, Group 2 (Chitosan) showed lowest SBS (11.01 ± 1.00 MPa). Intergroup comparison analysis presented that group 1, and group 4 (Co2 laser) (17.76 ± 0.41 MPa) displayed no significant difference in their bond integrity achieved. (p > 0.05). However, group 3 (Fotoenticine) (16.28 ± 0.51 MPa) and group 2 demonstrated comparable outcomes of SBS. (p > 0.05) ConclusionThe use of CHX and CO2 lasers as disinfectants on the CAD surface resulted in a positive impact on the SBS of resin composite, according to the study's findings. However, it is worth noting that Fotoenticine exhibited better antimicrobial efficacy against S. mutans