The high product yield of multi-branched core-shell Fe3-x O-4@Au magnetic nanoparticles was synthesized used as magnetic separation platform and surface-enhanced Raman scattering (SERS) substrates. The multi-branched magnetic nanoparticles were prepared by a seed-mediated growth approach using magnetic gold nanospheres as the seeds and subsequent reduction of metal salt with ascorbic acid in the presence of a stabilizing agent chitosan biopolymer and silver ions. The anisotropic growth of nanoparticles was observed in the presence of chitosan polymer matrix resulting in multi-branched nanoparticles with a diameter over 100 nm, and silver ions also play a crucial role on the growth of multi-branched nanoparticles. We propose the mechanism of the formation of multi-branched nanoparticles while the properties of nanoparticles embedded in chitosan matrix are discussed. The surface morphology of nanoparticles was characterized with transmission electron microscopy, scanning electron microscopy, ultraviolet visible spectroscopy (UV-Vis), X-ray diffraction, and fourier transform infrared spectroscopy and Fe-57 Mossbauer spectrometry. Additionally, the magnetic properties of the nanoparticles were also examined. We also demonstrated that the synthesized Fe3-x O-4@Au multi-branched nanoparticle is capable of targeted separation of pathogens from matrix and sensing as SERS substrates.