The exclusive properties of ionic liquids (ILs) offer various opportunities to develop advanced materials with appreciable therapeutic applications. Imidazolium-based ILs have been frequently used as reaction media and stabilizers for the development and surface functionalization of noble metal nanoparticles (NPs). This study reports the citrate-mediated reduction of silver ions in three different ILs, that is, 1-ethyl-3methylimidazolium methyl sulfate (and 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([BMIM][TFSI]). The resulting Ag-ILs NPs were characterized using many analytical techniques, including UV− visible spectroscopy, dynamic light scattering (DLS), scanning electron microscopy, Fourier transform infrared spectroscopy, and X-ray diffraction (XRD). DLS and XRD characterization revealed the negatively charged Ag-[EMIM][MS] NPs, Ag-[BMIM][OTf] NPs, and Ag-[BMIM][TFSI] NPs with mean hydrodynamic sizes of 278, 316, and 279 nm, respectively, and a face-centered cubic structure. These hybrid nanomaterials were subjected to in vitro antibacterial screening against three bacterial strains. The Ag-[BMIM][OTf] NPs exhibited significant activities against Escherichia coli, Staphylococcus aureus, and Enterobacter cloacae. The lowest inhibition concentration of 62.5 μg/mL was recorded against E. coli using Ag-[EMIM][MS] and Ag-[BMIM][OTf] NPs. Further, the density functional theory calculations carried out on the computed Ag-ILs in the gas phase and water showed relatively stable systems. Ag-[BMIM][TFSI] exhibited the lowest Gibbs free energy change of −34.41 kcal/mol. The value of the global electrophilicity index (ω = 0.1865 eV) for the Ag-[BMIM][OTf] correlated with its good antibacterial activity.