Inclusion complexation is one of the best strategies for developing a controlled release of a toxic drug without unexpected side effects from the very beginning of the administration to the target site. In this study, three benzimidazolium based ionic liquids (ILs) having bromide anion and cation bearing long alkyl chains, hexyl-([C 6 CFBim]Br), octyl-([C 8 CFBim]Br), and decyl-([C 10 CFBim]Br) were designed and synthesized as antibacterial drugs. Inclusion complexes (ICs) of studied ILs have been prepared by the combination of β-cyclodextrin (β-CD), considering these conjugations should enhance the benignity of ILs and make them potential candidates for the controlled drug release. Characterizations and structural analysis of studied ICs have been performed by 1 H NMR, 2D-ROESY NMR, FT-IR, HRMS, TGA, DSC, surface tension, ionic conductivity, dynamic light scattering (DLS), and isothermal titration calorimetry (ITC). Further, the morphology of the ICs has been analyzed by SEM and TEM. Furthermore, neat ILs and ICs have been treated against Escherichia coli and Bacillus subtilis to investigate their antibacterial activity, which confirms the prevention of bacterium growth and the shrinkage of the bacterial cell wall. The findings of this work provide the proof of concept that studied benzimidazolium based ILs-β-CD host−guest complexes should act as a potential candidate in controlled drug delivery and other biomedical applications.