The current study reports the modification of prokaryotic microorganism through a single-layer technique by using different polyanions/cations and doping with magnetic (Fe3O4) nanoparticles. Briefly, individual Escherichia coli cells were encapsulated through deposition of 1% sodium alginate as first layer followed by depositing precipitate layers of calcium chloride, disodium hydrogen phosphate, and Fe3O4 nanoparticles. Surface and cross sectional analysis of modified E. coli cells by field emission scanning electron microscope (FE-SEM) confirmed the synthesis of varying sizes of artificial shells around the microbial cells while the deposition of Fe3O4 nanoparticles was confirmed by transmission electron microscope (TEM). Thermogravimetric analysis (TGA) showed the deposition of 58 wt% of Fe3O4 nanoparticles on E. coli cell surface. Chemical structure analysis by Fourier transform infrared (FTIR) spectroscopy confirmed the presence of characteristic functional groups of deposited reagents in the hydrogel capsule. Zeta potential analysis of hydrogel capsule showed moderate stability with a surface charge of - 21 mV. Growth and viability analysis by Alamar Blue assay indicated marked increase in the reduction of resazurin blue (> 100%) by the modified E. coli indicating their viability. The movement and control of magnetized E. coli cells were manipulated using external permanent magnetic field as observed with optical microscope images. The surface-modified cells can find potential applications in bioremediation, biodegradation, and catalysis and can be used as biosorbents.