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Summary It is important to assess the biosafety of genetically engineered bacteria before release into the environment. In a previous study, the genetically engineered bacterium Burkholderia pyrrocinia JK‐SH007E1 was developed, showing biological control activity against a poplar canker disease. In the present work, the potential effects of B. pyrrocinia JK‐SH007E1 on soil microbial diversity and population structure in the poplar rhizosphere were assessed. The micro‐ecological effects of JK‐SH007E1 on soil microbial communities were investigated using substrate utilization assays (Biolog EcoPlate), enzyme activity assays and 16S rRNA sequencing to research species diversity and population structure of soil microbial communities. The genetically engineered isolate JK‐SH007E1 improved the functional diversity, soil enzyme activities and alpha diversity of soil microbial communities. However, the positive effects after inoculation attenuated with time, except for soil enzyme activities. Treatments with JK‐SH007 or JK‐SH007E1 were not different in impacts on soil enzyme activity and functional diversity of soil microbial communities. The results demonstrated that inoculation of JK‐SH007E1 into the poplar rhizosphere posed little or no threat to soil microbial communities in the long term. This work provides an additional insight into the effects of genetically engineered JK‐SH007E1 on the environment during long‐term use as biological control against poplar canker diseases.