Photodynamic therapy (PDT) is a clinically approved, non-invasive therapy currently used for several solid tumors, triggering cell death through the generation of reactive oxygen species (ROS). However, the hydrophobic nature of most of the photosensitizers used, such as chlorins, limits the overall effectiveness of PDT. To address this limitation, the use of nanocarriers seems to be a powerful approach. From this perspective, we have recently developed water-soluble and biocompatible, fluorescent, organic nanoparticles (FONPs) functionalized with purpurin-18 and its derivative, chlorin p6 (Cp6), as new PDT agents. In this study, we aimed to investigate the induced cell death mechanism mediated by these functionalized nanoparticles after PDT photoactivation. Our results show strong phototoxic effects of the FONPs[Cp6], mediated by intracellular ROS generation, and subcellular localization in HCT116 and HT-29 human colorectal cancer (CRC) cells. Additionally, we proved that, post-PDT, the FONPs[Cp6] induce apoptosis via the intrinsic mitochondrial pathway, as shown by the significant upregulation of the Bax/Bcl-2 ratio, the activation of caspases 9, 3, and 7, leading poly-ADP-ribose polymerase (PARP-1) cleavage, and DNA fragmentation. Our work demonstrates the photodynamic activity of these nanoparticles, making them promising candidates for the PDT treatment of CRC.