Dental caries, driven by dysbiosis in oral flora and acid accumulation, pose a significant threat to oral health. Traditional methods of managing dental biofilms using broad-spectrum antimicrobials and fluoride face limitations such as microbial resistance. Natural products, with their antimicrobial properties, present a promising solution for managing dental caries, yet their clinical application faces significant challenges, including low bioavailability, variable efficacy, and patient resistance due to sensory properties. Advanced drug delivery systems (DDSs) are emerging to address these limitations by enhancing the delivery and effectiveness of natural products. These systems, such as nanoparticles and micelles, aim to enhance drug solubility, stability, and targeted release, leading to increased therapeutic efficacy and decreased side effects. Furthermore, innovative approaches like pH-responsive nanoparticles offer controlled release triggered by the acidic environment of carious lesions. Despite these technological advancements, further validation is necessary for the clinical application of these DDSs.