The present study investigated the role of different doses of magnetic biochar (MBC, 0.65 to 6.7 g/L) in altering 2,2′,4,4′,5,5′hexabrominated diphenyl ether (BDE-153) accumulation and metabolism in rice by modulating iron plaque (IP) formation and the fatty acid (FA) profile as compared to biochar (BC). Both metabolomic and proteomic techniques were employed to further understand the molecular response in BDE-153-treated rice as affected by MBC co-exposure. Amendment with MBC enhanced IP formation by 3.0-and 2.5-fold as compared to BDE-153 and BC treatments, respectively. Treatment with MBC inhibited the FA content by up to 39.9% compared to BDE-153 alone, and a significant negative correlation between IP and total FA content (R 2 = 0.7851**) was found. Although there is no obvious dose dependency of MBC on BDE-153 accumulation in rice, the accumulation of BDE-153 in rice was inhibited by 31.4−81.9% upon exposure to different doses of MBC. The reductive debromination of BDE-153 on the root surface and inner roots was the greatest at 1.3 g/L MBC. The transfer of BDE-153 from the root surface to the inner root under MBC co-exposure was affected by root FAs and IP. MBC inhibited the expression of acyl carrier protein associated with FA synthesis, increased the expression of superoxide dismutase [Cu−Zn] and the content of FA 18:1 + 3O related to FAs metabolism, and consequently suppressed the FAs biosynthesis. In addition, IP formation under MBC treatments weakened the correlation between BDE-153 translocation and FA content. Taken together, these findings demonstrate the molecular mechanisms of BDE-153 accumulation and metabolism under MBC co-exposure and highlight the potential of this novel strategy for in situ remediation of BDE-153contaminated environments.