Background. Airborne transmission of endemic respiratory viruses, such as SARS-CoV-2 and influenza viruses, poses significant public health challenges. Aims. This manuscript investigates the efficacy of electromagnetic waves as a novel approach for airborne viruses inactivation in bioaerosol suspension, that is their natural route of transmission. Methods. Using a bioaerosol system in a controlled laboratory environment, different variants of SARS-CoV-2 and the human influenza virus were exposed to resonant radiated microwaves within safe power levels. Results. Radiated microwaves exposure led to a substantial reduction in the infectivity of highly transmissible SARS-CoV-2 variants, including the delta and omicron variants, achieving 80-90% reduction in infectivity. These variants exhibited susceptibility to the resonant radiated microwaves similar to the original Wuhan variant of SARS-CoV-2, confirming the effectiveness of this approach against a range of SARS-CoV-2 strains. Furthermore, the H1N1 human influenza virus displayed a 90% reduction in infectivity when exposed to microwave waves. However, the influenza virus exhibited distinctive response patterns, being susceptible to higher frequencies (up to 16 GHz) compared to SARS-CoV-2. Additionally, longer exposure times (5 minutes) were required to achieve the same level of inactivation observed in SARS-CoV-2. Conclusions: These findings highlight the potential of radiated microwaves as a strategy for inactivating SARS-CoV-2 and influenza viruses. Further, they contribute to determining the optimal frequencies, exposure times, and power levels required for effective virus inactivation. This innovative approach could provide valuable insights for developing sanitization strategies and public health interventions to mitigate the airborne transmission of respiratory viruses.