The role of magnetite in shaping microbial communities in natural biofilms and the mechanisms underlying pollutant degradation remain poorly understood. This study demonstrates that magnetite enhanced the degradation of 2,2',4,4'-tetrabrominated ether (BDE-47) in biofilms, with the highest removal rate of 82%. Magnetite promoted the production of extracellular polymeric substances and cytochrome c, enhanced the activity of electron transport system and conductivity, thus inducing the formation of electroactive biofilms. In addition, magnetite increased the bacterial diversity and altered the community composition of biofilms. Metagenomic and metatranscriptomic analyses demonstrated that magnetite specifically enriches genes and microorganisms associated with both mediated and direct interspecies electron transfer (IET), thereby accelerating IET process. Moreover, dissimilatory iron-reducing bacteria and dehalogenase-expressing microorganisms were enriched with magnetite, which facilitated BDE-47 degradation in the biofilms. These findings elucidate the impacts of magnetite on biofilms and the degradation mechanisms of BDE-47, providing theoretical basis for developing biofilm-based remediation technologies.