Amorphous silica particles (ASPs) have been reported to exhibit bioactive properties and are becoming the focus of attention as bioceramics. However, their interactions with proteins in living organisms remain to be understood and need to be investigated in order to achieve wider applications. Our research group found that chlorine (Cl)-containing ASPs are useful for protein immobilization. Photofunctional dyes (fluorescein (FS−), methylene blue (MB+)) that have the carboxy and amino groups as the main functional groups were immobilized on the Cl-containing ASPs via the mechanochemical method as the model molecule and their spectral properties were used to investigate and discuss the organic/inorganic interfacial bonding states. In FS−, the oxygen atoms of the carboxy groups in the molecule were immobilized by the hydrogen bonds with the silanol groups on the ASPs surfaces, indicating that there is an optimum Cl content for the immobilization as the monomer state. In the case of MB+, as the Cl concentration in the ASPs increases, the immobilization via the electrostatic interactions between the Cl in the ASPs and the terminal dimethylamino group, and the hydrogen bonding between the N atoms of the MB+ hetero ring and the particle silanol group were enhanced. These results mainly suggest that the protein adsorption system occurs through the hydrogen bonding between the carboxy groups of the protein and the silanol groups on the particles and via electrostatic interactions between the amino groups of the protein and the dissociated silanol groups and the contained Cl at the particles. Thus, the spectral characterization using dyes as probes is expected to predict the protein interactions with the amorphous silica particles.