Introduction: The emergence of the COVID-19 New Variant JN1 has heightened concerns regarding its transmission within dental settings. This study aimed to evaluate the efficacy of infection control protocols in preventing the spread of JN1 in dental clinics. The research addresses the urgent need to understand the effectiveness of these protocols against the variant in dental healthcare settings. Methods: Five diverse dental clinics were selected across different geographic regions. A total of 300 dental healthcare workers (HCWs) and 500 patients were enrolled in this prospective cohort study. Various infection control measures were implemented, including stringent hand hygiene, personal protective equipment (PPE) utilization, environmental disinfection, and aerosol management. Surveillance for COVID-19 cases among participants was conducted using regular polymerase chain reaction (PCR) testing. Transmission rates were compared among clinics employing different infection control measures. Results: Clinics implementing comprehensive infection control measures demonstrated significantly lower transmission rates compared to those with specific or no measures. The transmission rates varied: stringent hand hygiene and PPE utilization clinics reported rates around 8%, while those focusing solely on environmental disinfection or aerosol management showed intermediate rates. Demographic analysis revealed variances in affected individuals' profiles across clinics. Conclusion: Tailored approaches incorporating comprehensive measures such as stringent hand hygiene, PPE utilization, environmental disinfection, and aerosol management are crucial for effective prevention. Compliance and challenges in implementation highlight the necessity for tailored strategies.