A progressive way in photodynamic therapy is to design photosensitive agents that may operate at lower optical power. Hybrid organic–inorganic silver-, iron-, and silver&iron-contained nanoparticles (NPs) were synthesized using H. perforatum extract and explored as photosensitizers for anticancer and antimicrobial photodynamic therapies at ultra-low power light (2.30 mW/cm2). Hybrid silver- and silver&iron-contained NPs revealed the most promising results for anticancer photodynamic therapy: at a concentration of 25 μg/mL, the difference between viability of non-radiated and irradiated HeLa cells was up to 71%. Importantly, HeLa cancer cells are more assailable for hybrid NP activity than the normal fibroblast MSU-1.1 cell line, which was observed at both “dark” cytotoxicity and DCFH-DA assays. Oxidative stress induced by hybrid iron- and silver&iron-contained NPs in cancer HeLa cells is higher (≥1.7 times) than that in normal fibroblast MSU-1.1 cells. For antimicrobial photodynamic therapy, hybrid silver&iron-contained NPs (at a concentration of 25 μg/mL) were found to be promising photosensitizers being bacteriostatic against E. coli and S. aureus in the “dark” condition and bactericidal after light irradiation. Antimicrobial properties of hybrid silver&iron-contained NPs are the result of synergy of antimicrobial activities of H. perforatum and silver. The highest efficiency against bacteria is achieved at concentrations and conditions at which H. perforatum and silver NPs apart were less or not active. Furthermore, hybrid silver&iron-contained NPs combine photodynamic activities against cancer and bacteria cells with the ability to enhance magnetic resonance imaging (MRI) contrast. This combination makes these NPs promising materials for biomedical application at ultra-low power photodynamic therapy of near-surface cancer or inflammatory disorders, with the possibility of their visualization using MRI.