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Polybrominated diphenyl ethers (PBDEs) are toxic to humans and can easily accumulate in the environment. Nanoscale zero-valent iron (NZVI) and modified NZVI have been developed to remediate PBDE contamination. However, their degradation in soil systems and their microbial toxicity have not been widely explored. In this study, NZVI supported on biomass carbon was applied to remove decabromodiphenyl ether (BDE-209) from contaminated soil. A removal efficiency of 100% was achieved within 384 h as BDE-209 reacted with 0.10 g/g soil biomass carbon NZVI particles (BC–NZVI) at pH 7.00. The reaction followed pseudo-first-order kinetics, and the BDE-209 removal efficiency increased with increasing BC–NZVI dosage and decreasing initial BDE-209 concentration, pH, and moisture content. Biological activity assays (dehydrogenase activity and soil basal respiration) were conducted to provide a preliminary risk assessment of the BC–NZVI application in BDE-209 contaminated soil. The results demonstrate that BC–NZVI has a strong potential for in situ remediation of organic-contaminated soil.