The most challenging and wanted development in photodynamic therapy is the control of photosensitizer (PS) cytolocalization and the mechanism of cell death. 5,10,15-triphenyl-20-(3-N-methylpyridinium-yl)porphyrin (3MMe) administered to HeLa cells as DMSO solution accumulates in the cytoplasmic membrane (CM) where it causes severe photodamage and cell necrosis. In contrast, when incorporated in marine atelocollagen/xantham gum polymeric nanocapsules, the PS is shuttled through CM allowing its gradual release and accumulation in mitochondria and lysosomes. Little photodamage was caused to cells in this case, but compelling evidences are presented showing that encapsulation changes the cytolocalization and shifts the cell death mechanism from necrosis to apoptosis. In conclusion, both of those challenges can be overcome by encapsulation of typical PSs such as 3MMe by using the new concept of photodynamic treatment with minimal cell damage by targeting specifically some key organelles. We are confident that these findings are important for the development of more efficient photosensitizers tailored to induce apoptosis while minimizing undesirable side effects such as over-inflammation.