The aim of this study was to synthesize in high product yield of anisotropic core-shell Fe3O4@Au magnetic nanoparticles and to investigate the effect of the immunomagnetic separation (IMS) volume on the capture efficiency. For these purposes and for the first time, we synthesized polyhedral magnetic nanoparticles composed of Fe3O4 core Au shell. To synthesize magnetic gold anisotropic core-shell particles, the seed-mediated synthetic method was carried out. By choosing an appropriate amount of iron particles and growth solution the fine control of the seed-mediated approach is enabled. This led to the high product yield of anisotropic nanoparticles. The magnetic separation of these nanoparticles was easily accomplished, and the resulting nanoparticles were characterized with transmission electron microscopy (TEM), ultraviolet visible spectroscopy (UV-vis), near edge absorption fine structure (NEXAFS) spectroscopy, and X-ray diffraction (XRD). Additionally, the magnetic properties of the nanoparticles were examined. The magnetic nanoparticles (MNPs) were modified with antibody and interacted with Escherichia coli (E. coli). The high capture efficiency between the magnetic nanoparticles and E. coli is evidenced by SEM images. The capture efficiency decreases with an increase of volumes, and the highest capture efficiency was observed for E. coli in an experiment volume of 100 L for magnetic nanoparticles. The percentage of captured E. coli for polyhedral nanoparticles was found to be approximately 95 % and for spherical nanoparticles 88 %, respectively.