Nano-magnetic MnFe2O4 was prepared and examined to immobilize Cr(VI) in the soil. According to the results of scanning electron microscopy (SEM) and X-ray diffraction (XRD) the formation of nano-magnetic MnFe2O4 with the particle size of less than 200 nm was demonstrated. Compared with the untreated soil, the leachability of Cr (VI) was reduced from 70.95% to 4.22% through toxicity characteristic leaching procedure (TCLP) at a dosage of 2 g/L of nanoparticles and 192 h remediation time. At the same condition, the physiologically based extraction test (PBET) human bioaccessibility of chromium was reduced from 86.76% to 4.42%. Moreover, the plant bioavailability of hexavalent chromium (using EDTA) was reduced from 83.72% to 5.53%. According to the sequential extraction procedure (SEP) the loosely bounds Cr (90.28%) was converted to the relatively strong bound (Fe-Mn oxides fraction, 92.09%) revealed the significant decrease in risk of release and availability of chromium after immobilization procedure. Further, results of column experiments of Cr(VI) elution revealed that almost all of the water-soluble chromium was converted to the associated synthesized nanoparticles phase. Overall, the present study proved that nano-magnetic MnFe2O4 significantly enhanced the hexavalent chromium immobilization through a decrease in leachability, plant bioavailability, human bioaccessibility, and risk of release.