The functions of extracellular polymeric substances (EPS) during the adhesion of Bacillus subtilis to kaolinite, montmorillonite, and goethite were examined by a direct comparison of the adhesion behaviors of native and EPS-free cells via cation exchange resin (CER) treatment using batch experiments, attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy, and potentiometric titration. The EPS removal had no apparent influence on bacterial adhesion when the wet bacteria/mineral mass ratio was low (<0.4 for the clay mineral systems and <1.8 for the goethite system). With higher mass ratios, the absence of EPS reduced adhesion to clay minerals but enhanced adhesion to goethite. The ATR-FTIR spectra suggested that protein conformational changes were involved in the adhesion of bacteria to clay minerals, whereas additional chemical interactions such as POFe bonds were important for adhesion to goethite. In addition to electrostatic forces (repulsion for clays and attraction for goethite), absence of chemical interactions may also cause the relatively much weaker bacterial adhesion to clay minerals than to goethite. The absence of EPS did not change the interaction mode of the adhesion to clay minerals but enhanced the chemical interactions via carboxyl groups for bacteria–goethite adhesion. The potentiometric titration results coupled with the ATR-FTIR spectra showed a significant increase in site concentrations of the CER-treated bacteria as compared to the native cells. Changes in surface site concentrations and chemical interactions that were accompanied by the EPS removal may reasonably explain the influences of EPS on bacterial adhesion to different minerals.