Infection control is essential for the success of prosthodontic and oral implant procedures, as microbial contamination can lead to serious complications such as denture stomatitis and peri-implantitis. While synthetic disinfectants like chlorhexidine are commonly used, they may cause side effects including irritation, toxicity, and the development of microbial resistance over time. Natural products derived from plants, animals, and minerals are currently being explored as safer alternatives. Compounds such as epigallocatechin gallate from green tea; eugenol from clove oil; quercetin, thymol, cinnamaldehyde, and flavonoids from propolis; and terpinen-4-ol from tea tree oil have shown strong antimicrobial and anti-biofilm properties. These natural agents are not only effective against harmful oral bacteria but also promote healing, are more biocompatible, environmentally friendly, and are often preferred by patients. However, challenges remain regarding their routine clinical use. The strength and composition of natural agents can vary, and there is a lack of consistent product standards, clinical trials, and comprehensive safety data. Currently, these products are not approved by the U.S. Food and Drug Administration for dental use and are only available as over-the-counter remedies. Production costs and scalability must also be evaluated in comparison with synthetic alternatives. Emerging technologies, such as nanocarriers and targeted delivery systems, are being developed to enhance the effectiveness of natural agents in dental applications. Further clinical research and the establishment of clear regulatory guidelines are necessary to support their integration into clinical practice. Natural disinfectants hold significant potential to become valuable, safe, and sustainable tools for maintaining hygiene in prosthodontics and oral implantology.