Photodynamic therapy (PDT) is a clinically established approach that relies on the localized generation of reactive oxygen species (ROS) mediated by a photosensitizer (PS), light, and molecular oxygen. Protoporphyrin IX (PpIX) is an approved PS; however, its intracellular retention is limited, factor that can alter its overall photodynamic efficiency. In this study, we report how the design of PpIX derivatives bearing piperazine (PpIX-Pip) or morpholine (PpIX-Morp) substituents may modulate lipophilicity, cellular uptake, oxidative stress, and phototoxicity. The photodynamic activity of these derivatives was evaluated in the aggressive triple-negative human breast cancer cell line MDA-MB-231. Both derivatives showed greater time-dependent cellular retention and enhanced photodynamic activity compared to PpIX, promoting oxidative stress, and triggering loss of mitochondrial membrane potential and caspase-3 activation. These results highlight the impact of rational structural modification of PpIX on photodynamic efficiency and provide valuable structure-activity relationship insights for the development of improved porphyrin-based PS for PDT.