Cold atmospheric plasmas offer a non-thermal chemical-free technology of bio-decontamination. Compared to their antibacterial effects, the plasma-based antiviral mechanisms remain poorly studied, hampering their promising widespread application. Here, the robust Adeno-Associated Viral (AAV) vector was used as a model to investigate the plasma virucidal effects. AAV inactivation was analyzed by in vitro testing of virus infectivity, vector genome quantification, and vector capsid integrity. It was found that plasma treatment for 10 min resulted in at least a 3-log 10 reduction in AAV6 infectious activity. The acidification and enrichment in nitrites and nitrates characterized plasma-activated phosphate-buffered saline. The results suggest that oxidative and nitrosative damage to the viral capsid proteins, along with partial genome degradation, accounted for the loss of AAV6 infectivity. Collectively, these findings demonstrate the inactivation capacity of plasma-generated reactive nitrogen species for AAV6 and support their potential use in disinfection strategies applicable to non-enveloped viruses such as AAV.