This study aims to assess the potential bacterial inactivation pathway triggered by argon (Ar) cold atmospheric pressure plasma jet (CAPJ) discharge using spectroscopic and imaging techniques. Electrical and reactive species of the Ar CAPJ discharge was characterized. The chemical composition and morphology of bacteria pre- and post-CAPJ exposure were assessed using Fourier transform infrared (FTIR), Raman micro-spectroscopy, and transmission electron microscopy (TEM). A greater than 6 log reduction of E. coli and S. aureus was achieved within 60 and 120 s of CAPJ exposure, respectively. Extremely low D- values (< 20 s) were recorded for both the isolates. The alterations in the FTIR spectra and Raman micro-spectra signals of post-CAPJ exposed bacteria revealed the degree of destruction at the molecular level, such as lipid peroxidation, protein oxidation, bond breakages, etc. Further, TEM images of exposed bacteria indicated the incurred damages on cell morphology by CAPJ reactive species. Also, the inactivation process varied for both isolates, as evidenced by the correlation between the inactivation curve and FTIR spectra. It was observed that the identified gas-phase reactive species, such as Ar I, O I, OH•, NO+, OH+, NO2-, NO3-, etc. played a significant role in bacterial inactivation. This study clearly demonstrated the effect of CAPJ exposure on bacterial cell morphology and molecular composition, illuminating potential bacterial inactivation mechanisms.