This work reports two different strategies for the formation of hybrid microbeads using chitosan and polyethylene glycol (PEG) as based biodegradable materials for radiation shielding. An organic–inorganic hydrogel was prepared by ionotropic gelation. During the in-situ loading, incorporating magnetic nanoparticles Fe2O3 into the polymer matrix, magnetic nanostructures, were entrapped in the polymer matrix during the physical cross-linking of the polymer with the physical cross-linker (sodium triphosphate). However, in case of post-loading mechanism the loaded nanoparticles favor the precipitation on the surface of the formed beads. We use different characterization techniques for our systems such as scanning electron microscopy (SEM), x-ray, infrared spectroscopy (XRD), and X-ray radiation shielding application. The results demonstrate that by incorporating nanostructured magnetic particles into the polymer matrix, the surface morphology based on the two processes allow the magnetic nanoparticles to be embedded or form an outer shell and precipitated on the surface of polymer microbeads. The values of μ for the hydrogels loaded with Fe2O3 by in-situ process have the larger values of the linear coefficient however, in case of post-loading process the values dramatically decrease in compare with the in-situ ones at the same tube voltage. The presented work recommended as a good mentor for radiation shielding.