The aim of study was to evaluate the application of casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) and fluoride regarding their effect on the shear bond strength (SBS), bond failure pattern of brackets using the adhesive remnant index (ARI) and assessing the quality of enamel surface using the enamel damage index (EDI). Sixty extracted premolar teeth were randomly divided into four groups regarding pretreatment application of CPP-ACP and fluoride. Brackets were bonded using the conventional method. Specimens were thermocycled for 1000 cycles and were subsequently tested for the SBS in a universal testing machine. After debonding, the teeth were examined under a stereomicroscope to evaluate the ARI. Then, The EDI was assessed using a scanning electron microscope (SEM). Data were analyzed using ANOVA and the Chi-square test. Evaluation of SBS, ARI and EDI scores showed no significant difference among the study groups. However, a correlation was found between the ARI and EDI scores, indicating that with more adhesive remnants on enamel surface, enamel damage was lower. The use of CPP-ACP and fluoride can be considered a prophylactic application since these agents did not compromise bracket bond strength although they did not reduce iatrogenic damage to the enamel.