In the present study, the novel shell nanostructures of Cu-MOF compound were synthesized for the first time by effective, fast and controllable method of ultrasonic assisted reverse micelle. The Fe3O4 nanoparticle was used as core for improving the physicochemical properties and also the stability of these compounds. The results showed that Fe3O4@Cu-MOF/core-shell nanostructures have significant thermal stability compared to pure Cu-MOF samples. In fact, the TEM study verified the development of core shell nanostructures. The EDS with mapping has been applied to be sure about the existence of related elements in the final Fe3O4@Cu-MOF/core-shell nanostructure. The design of the fractional test was used to change the antibacterial properties of these compounds. This method of optimization generates structures with a high surface area that affect the antibacterial properties of the materials. Systematic studies applied in this study, as well as optimization processes, can be developed as a new strategy for controlling the physicochemical properties of the products. Fe3O4@Cu-MOF/core-shell nanostructures have shown reasonably good antibacterial activities against both Gram-positive and Gram-negative bacteria. © 2020 Elsevier Inc.