Mineral-microbe interactions are widespread in a number of environmental processes such as mineral weathering, decomposition, and transformation. Both clay minerals and silicate-weathering bacteria are widely distributed in nature, and the latter contribute to weathering, diagenesis, and mineralization of major rock-forming minerals. The purpose of this study was to observe changes in the chemical composition and structure, especially the phase transformation, of smectite after processing by a silicate-weathering bacterium. The interaction between Bacillus mucilaginosus and bentonite was studied using custom culture media. Results from Inductively Coupled Plasma-Atomic Emission Spectrometry revealed that the bacterium promoted release of Si and Al from solid bentonite to solution. Concomitantly, the K and Fe contents of the mineral increased as shown by X-ray photoelectron spectroscopy results. After interaction with the bacterium, the montmorillonite underwent a possible structure transformation to smectite, as indicated by the emergence of a new weak peak (d = 9.08 A ° ) shown by X-ray diffraction patterns. The mineralogical changes were also demonstrated by the decrease in the specific surface area of the mineral from 33.0 to 24.0 m2/g (these lower values for SSA of bentonite are related to the particle size of the smectite examined (120–160 mesh) and the weakened absorption bands in Al–O–H and Si–O–Si vibrations by Micro Fourier-transform infrared spectroscopy. The morphology changes in the bacteria observed by environmental scanning electron microscopy and atomic force microscopy revealed an obvious growth of the flagella in the presence of bentonite.