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As concerns about public health and environmental problems regarding contamination by toxic substances increase worldwide, the development of a highly effective and specific treatment method is imperative. Although physicochemical arsenic treatment methods have been developed, microbial in vivo remediation processes using live cell fabricated nanoparticles have not yet been reported. Herein, we report the development of magnetic iron nanoparticles immobilized an extremophilic microorganism, Deinococcus radiodurans R1, capable of removing toxic arsenic species. First, in vivo synthesis of magnetic iron nanoparticles was successfully achieved with the D. radiodurans R1 strain and characterized by scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDX), dynamic light scattering (DLS), zeta-potential, Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) analysis. Second, the maximum removal capacity of the magnetic iron nanoparticle-immobilized D. radiodurans R1 strain (DR-FeNPs) for arsenic [As(V)] was evaluated under the optimized conditions. Finally, the removal capacity of DR-FeNPs in the presence of various competitive anions was also investigated to simulate the practical application. More than 98% of As(V) was efficiently removed by DR-FeNPs within 1 h, and the removal efficiency was stably maintained for up to 32 h (98.97%). Furthermore, the possibility of recovery of DR-FeNPs after use was also suggested using magnets as a proof-of-concept.