The selectivity of antimicrobial photodynamic therapy (PDT) can be enhanced by coupling the photosensitizer (PS) to a targeting ligand. Nanoplatforms provide a medium for designing delivery vehicles that incorporate both functional attributes. We report here the photodynamic inactivation of a pathogenic bacterium, Stapkylococcus aureus, using targeted nanoplatforms conjugated to a photosensitizer (PS). Both electrostatic and complementary biological interactions were used to mediate targeting. Genetic constructs of a protein cage architecture allowed site-specific chemical functionalization with the PS and facilitated dual functionalization with the PS and the targeting ligand. These results demonstrate that protein cage architectures can serve as versatile templates for engineering nanoplatforms for targeted antimicrobial PDT.