Pathogenic microbes are becoming one of the biggest health-threatening challenges leading to a global need for sustainable solutions. Ultraviolet (UV) radiation enables the control of microorganismal replication. However, microbes with protected and/or repairable nucleic acids have challenged the inactivation efficacy of current UV sources. Targeting proteins responsible for nucleic acid protection and repair or microbial infection can be game-changing. Here, we identified and kinetic-modelled the efficiency of a new mercury-free radiation technology: microplasma UV, which radiates around proteins’ UV-absorption and decomposition peak with unique spectral power distributions. Surrogates for challenging microorganisms were studied: Escherichia coli (E. coli) bacterium that contains nucleic acid reactivation proteins, and bacteriophage-MS2 virus that possesses viral proteins responsible for protecting nucleic acid (capsid) and initiating infection (maturation). The microplasma UV lamp photons, at wavelengths below 240 nm, induced nucleic acid repair-deficiency disorder and enhanced inactivation of viral infectivity. Both studied microplasma UV sources presented higher germicidal efficiency for MS2 and significantly lower repair for E. coli compared with the standard values reported for mercury UVC lamps and UVC light emitting diodes (UVC-LEDs) in the literature. The reactive oxygen species were found to not play a role in this enhancement. The present results introduce promising UV sources for efficient and long-lasting microbial inactivation, thereby paving the way toward sustainable disinfection systems.