This study describes an efficient antimicrobial drug delivery system composed of iron oxide magnetic nanoparticles (Fe3O4 NPs) coated by an MOF-199 network. Then, the prepared vancomycin (VAN)-loaded carrier was fully packed in a lattice of beta-cyclodextrin (BCD). For cell adhesion, beta-cyclodextrin has been functionalized with guanidine (Gn) groups within in situ synthetic processes. Afterward, drug loading efficiency and the release patterns were investigated through precise analytical methods. Confocal microscopy has shown that the prepared cargo (formulated as [VAN@Fe3O4/MOF-199]BCD-Gn) could be attached to the Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) bacterial cells in a higher rate than the individual VAN. The presented system considerably increased the antibacterial effects of the VAN with a lower dosage of drug. The cellular experiments such as the zone of inhibition and optical density (OD600) have confirmed the enhanced antibacterial effect of the designed cargo. In addition, the MIC/MBC (minimum inhibitory and bactericidal concentrations) values have been estimated for the prepared cargo compared to the individual VAN, revealing high antimicrobial potency of the VAN@Fe3O4/MOF-199]BCD-Gn cargo.