Background: The emergence of the JN1 variant of SARS-CoV-2 has raised concerns about transmission within dental settings, prompting a need to assess the effectiveness of infection control strategies. Methods: A prospective cohort study was conducted across multiple dental clinics to evaluate the impact of infection control measures on JN1 transmission rates. Assessments included compliance with ventilation, PPE usage, patient screening, disinfection protocols, and molecular analysis of viral samples. Results: Implementation of stringent infection control measures showed a significant correlation with reduced transmission of the JN1 variant within dental settings. Strong negative correlations were observed between compliance with ventilation, PPE adherence, and physical distancing with reduced transmission rates. Conclusion: This study highlights the crucial role of robust infection control strategies, including ventilation, PPE adherence, and physical distancing, in mitigating the spread of the JN1 variant in dental settings. Continuous vigilance and adaptation to evolving variants are imperative to sustain these positive outcomes.