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Plant-microbe interactions have been effectively used in phytoremediation to reduce agrochemical contamination of crops and soils, but little information is available regarding the general effect of such association on rhizosphere soil homeostasis. In this study, we immobilized Stenotrophomonas pavanii DJL-M3, a carbendazim (CBZ)-degrading endophyte, in rice husk-derived biochar to control fungicide residue in the rice microenvironment. The influence of biochar inoculated with strain DJL-M3 on rhizobacterial communities was also investigated, including activity and fundamental function predictions. An adsorption kinetics test showed that strain DJL-M3 slowed the adsorption rate slightly without sacrificing the adsorption capacity of rice-husk biochar on CBZ. Immobilization in biochar helped S. pavanii DJL-M3 to establish an ecological niche in rhizosphere soils. This process significantly reduced CBZ levels in rice and rhizosphere soil while maintaining stable heterotrophic microbial respiration and carbon (C) metabolic activity. Soil amendment with the strain DJL-M3-biochar composite resulted in relatively little disturbance of fundamental soil functions, such as nitrogen (N) and sulfur (S) cycling, which explained the better plant growth and higher soil fertility observed with CBZ contamination. Overall, the combination of biochar and S. pavanii DJL-M3 demonstrated the potential to safeguard the microbiological environment of rice., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Fayun Feng reports financial support was provided by National Natural Science Foundation of China. Fayun Feng reports financial support was provided by Jiangsu Agricultural Science and Technology Independent Innovation Fund. Honjie Sheng reports financial support was provided by National Natural Science Foundation of China., (Copyright © 2023 Elsevier Ltd. All rights reserved.)