The continued and increasing adoption of genetically modified plants (GMPs) in agriculture has raised both perspectives on increasing the productivity and some concern over their potential effects on the environment, especially on soil. These effects include unintentional changes in the chemical compositions of root exudates, and the direct or indirect effects of transgenic plants on non-target species of soil micro-organisms that have a key role in the maintenance of soil quality and environmental sustainability. Therefore any change to the quality of crop residues and rhizosphere inputs could modify the dynamics of the composition and activity of organisms in soil. One of the most common transgenic traits in commercial GMPs is insect resistance based on the expression of Cry toxin derived from Bacillus thuringiensis (Bt), and it is crucial that risk assessment studies on the use of Bt crops consider the impacts on micro-organisms in soil. This review summarizes the results of most of the studies that have been conducted to specifically test the effects of Bt plants on soil microbial communities, and examines the role of soil properties as one of the most important factors to be considered to study the interactions between micro-organisms and Bt plants. Most studies suggest that the Bt plants that have been released for commercial purposes could cause small changes in microbial communities and these are often transient in duration. However, experimental results are often contrasting and, given our limited knowledge of the soil system and the linkage with the soil microbial community's diversity and function, more work needs to be done on a case-by-case basis to further evaluate the effects of Bt plants on soil micro-organisms and soil ecosystem functions.