Expansive soils, characterized by large montmorillonite (Mnt) contents, exhibit significant swelling-shrinkage behavior, posing engineering challenges in regions with alternating wet and dry seasons, such as southern China. Recent studies have explored the possible use of microbes to control or modify the swelling-shrinkage behavior. This study has evaluated microbial influence on the swelling-shrinkage behaviors of expansive soils. A combination of aqueous phase characterization through inductively coupled plasma-optical emission spectroscopy (ICP-OES) and solid phase analyses including X-ray diffraction (XRD) and Fourier-transform infrared spectroscopy (FTIR) was adopted to elucidate the variations in system parameters. Results showed that Si, Al, K, and Mg concentrations in the supernatant increased with prolonged interaction, with K concentration peaking at 14 days and decreasing to 27.5 mg L−1 at 42 days, indicating K+ uptake by Mnt interlayers. The Si–O bonds in tetrahedral sheets, Al–O bonds in octahedral structures, and –OH bonds in water molecules were disrupted by Paenibacillus mucilaginosus, accelerating the montmorillonite to illite (Mnt-to-Ilt) transformation. An Ilt-Mnt interstratification peak appeared near 9.88°2θ after 14 days, and an Ilt peak emerged at 48.07°2θ after 28 days. The Mnt content decreased by 37.28%, while the Ilt content increased by 104.01% after 42 days, as calculated by the K-value method. Analysis of swelling-shrinkage properties revealed that reduced Mnt content led to a 69.01% decrease in the free swell index and a 24.04% decrease in the swell ratio under load. The linear and volumetric shrinkage ratios decreased by 32.90% and 30.98%, respectively. Microorganisms can promote the weathering and phase transformation of Mnt into non-expansive minerals, thereby reducing the amount of it and thus reducing the swelling-shrinkage potential in expansive soils.