Biochar-immobilized microbial technologies hold substantial promise for the remediation of environmental contaminants. However, the understanding of remediation efficiency and the operation of microbial consortia in complex soil environments using biochar as a carrier remains limited. In this study, we explored the impacts of biochar combined with bacterial consortium QY2Y (consisting of Chitinophaga sp. MH-1, Achromobacter sp. YH-1, Methylobacterium sp. ZY-1, and Sphingomonas sp. GY-1) on BDE-47 dissipation in contaminated soil, as well as its effects on soil-plant systems. The findings indicated that the immobilization of biochar and QY2Y not only stimulated the biodegradation of BDE-47 (61.50%) but also decreased the bioavailability of BDE-47, subsequently reducing the concentration of BDE-47 in the edible portion of rapeseed (Brassica napus L.) by 82.00%. In addition, the combined treatment notably increased soil pH, enhanced the physicochemical properties and nutrient conditions of the soil, and amplified soil dehydrogenase, catalase, urease, and acid phosphatase activities by 58.72%, 69.25%, 54.24%, and 74.74%, respectively. The application of biochar-based QY2Y improved the soil microbial community structure, bolstered the interspecific symbiotic and cooperative relationships, and restructured the keystone taxa. The key species microbes had direct and significant positive effects on BDE-47 degradation, soil nutrients, and soil enzyme activity. This study deepens our understanding of the potential applications of immobilized microbial consortia in treating PBDE-contaminated soils and offers guidance for the management and remediation of contaminated soils.