By allowing visualization of submitochondrial protein distributions, fluorescence nanoscopy offers significant advantages for understanding cell death control. How cells manage, and control mitochondrial intermembrane proteins involved in apoptosis, such as Cytochrome c and DIABLO/SMAC is not completely defined. In this study, we used two-color STED nanoscopy to gain insight into the submitochondrial distribution of Cytochrome c and DIABLO/SMAC, two apoptotic effectors. Proteotoxic stress was used to induce cell death in leiomyosarcoma cells. STED microscopy allowed to reveal a cluster organization of DIABLO/SMAC distribution compared to the uniform distribution of ATP synthase. These clusters sometimes co-localize with clusters containing Cytochrome c. In conclusion, within the intermembrane space of mitochondria different storages of pro-death effectors exist.