Photocatalysts have recently attracted attention for removing infectious-disease-causing bacteria and viruses. Among such photocatalysts, ground Rh-doped SrTiO3 (“g-STO:Rh”) has been found to have biospecificity that reduces the Qβ phage infectivity under conditions that did not decrease the E. coli survival rate. Elucidating the mechanism of selective antiphage activation is important for developing photocatalysts that act effectively against specific microorganisms. In this study, SDS-PAGE and quantitative PCR showed that a g-STO:Rh-treated Qβ phage preferentially inactivated the A2 protein involved in attachment to host cells. The analysis of the photocatalyst-treated ovalbumin using g-STO:Rh indicated that the protein’s isoelectric point significantly influenced the initial interaction with g-STO:Rh. However, once the protein is absorbed, it was decomposed without the release of intermediates. Furthermore, an inactivation assay for four different phages by photocatalyst treatment using g-STO:Rh revealed that phages with positively charged proteins are highly susceptible to inactivation, and the accessibility of critical components to g-STO:Rh influences susceptibility. We conclude that the selective antiphage activation of g-STO:Rh depends on the adsorption efficiency of the protein and g-STO:Rh.