Regularly removing biofilm and controlling risk factors are essential to the individual and the clinician for managing dental caries. Researchers have investigated antimicrobial agents to counter the bacterial component in the caries process to prevent and manage the disease. However, these agents are considered to have limited value and are therefore restricted to special care groups. This chapter summarises the effect of antimicrobial agents such as chlorhexidine, iodine and ozone as well as the antimicrobial effect of natural products on managing carious lesion development.