Since their invention, periodic mesoporous organosilicas (PMOs), an innovative class of materials based on organic as well as inorganic hybrid nanocomposites, have gathered enormous interest owing to their advantageous physicochemical attributes over the pristine mesoporous silica nanoparticles (MSNs). To further increase the interactions with the therapeutic guest species and subsequent compatibility as well as the physicochemical properties of PMOs, we demonstrate the post-hydroxylation of benzene-bridged PMO-based nanoparticles for photodynamic therapy (PDT). Initially, the hydrophobic benzene group in the PMO framework is modified through electrophilic substitution-assisted hydroxylation mediated by Fenton as well as Fenton-like reactions utilizing divalent and trivalent metal salts, respectively. These post-grafted PMOs with tuned hydrophobicity resulted in improved biocompatibility as well as drug loading efficiency through governing the interactions in host-guest chemistry by changing the physicochemical properties of the PMO frameworks. Furthermore, the photosensitizer, protoporphyrin IX (PpIX) molecules, encapsulated in the PMO frameworks showed a significant PDT effect in colon carcinoma (HT-29 cell line) and Gram-negative bacterial strain, Escherichia coli (E. coli). Furthermore, the light-induced cytotoxic properties in vitro are confirmed by various tests, including lactate dehydrogenase (LDH) assay for cell membrane damage and caspase assay for apoptosis determination. Indeed, the delivered PpIX molecules from PMOs generated deadly singlet oxygen species intracellularly under visible light irradiation, resulting in cell death through concomitantly triggered apoptotic caspases. Together, our findings demonstrate that this post-modified PMO design is highly advantageous and can be used as an effective PDT platform.