A series of phthalocyanine-peptide-quencher conjugates (6–9) were synthesized as photosensitizers for photodynamic therapy in cancer treatment. The photophysical, photochemical and photobiological properties of these activatable molecular beacons were also investigated in this study. For this purpose, the fluorescence, singlet oxygen and photodegradation quantum yields and fluorescence lifetime values of the compounds were determined in DMSO solutions. The phototoxicity and cytotoxicity of the systems were studied against the cervical cancer cell line named HeLa for an evaluation of their suitability for photodynamic therapy. The results showed that a maximum of 80% of HeLa cells were killed following light irradiation with photodynamic efficiency. All of the results showed that the novel activatable molecular beacons could be suitable candidates for cancer treatment via PDT technique.