Biofilm-related infections of the oral cavity, including dental caries and periodontitis, represent the most prevalent health problems. For years, the treatment thereof was largely based on antibacterial chemical agents. Recently, however, there has been growing interest in the application of more preventive and minimally invasive biotechnological methods. This review focuses on the potential applications of enzymes in the treatment and prevention of oral diseases. Dental plaque is a microbial community that develops on the tooth surface, embedded in a matrix of extracellular polymeric substances of bacterial and host origin. Both cariogenic microorganisms and the key components of oral biofilm matrix may be the targets of the enzymes. Oxidative salivary enzymes inhibit or limit the growth of oral pathogens, thereby supporting the natural host defense system; polysaccharide hydrolases (mutanases and dextranases) degrade important carbohydrate components of the biofilm matrix, whereas proteases disrupt bacterial adhesion to oral surfaces or affect cell-cell interactions. The efficiency of the enzymes in in vitro and in vivo studies, advantages and limitations, as well as future perspectives for improving the enzymatic strategy are discussed.