Mitochondrial outer membrane permeabilization (MOMP) is a core event in apoptosis signaling. However, the underlying mechanism of BAX and BAK pore formation remains incompletely understood. We demonstrate that mitochondria are globally and dynamically targeted by endolysosomes (ELs) during MOMP. In response to pro-apoptotic BH3-only protein signaling and pharmacological MOMP induction, ELs increasingly form transient contacts with mitochondria. Subsequently, ELs rapidly accumulate within the entire mitochondrial compartment. This switch-like accumulation period temporally coincides with mitochondrial BAX clustering and cytochrome c release. Remarkably, interactions of ELs with mitochondria control BAX recruitment and pore formation. Knockdown of Rab5A, Rab5C, or USP15 interferes with EL targeting of mitochondria and functionally uncouples BAX clustering from cytochrome c release, while knockdown of the Rab5 exchange factor Rabex-5 impairs both BAX clustering and cytochrome c release. Together, these data reveal that EL-mitochondrial inter-organelle communication is an integral regulatory component of functional MOMP execution during cellular apoptosis signaling. Display omitted •EL targeting of mitochondria is a common feature during apoptosis signaling•Knockdown of Rab5 or USP15 uncouples BAX clustering from MOMP•Rab5 GEF Rabex-5 regulates MOMP upstream of BAX recruitment•EL transformation of mitochondria positively regulates BAX-mediated MOMP Wang et al. show that upon activation of regulated cell death, endolysosomal vesicles (ELs) are targeted to mitochondria prior to and during their permeabilization by BAX-mediated pores. These inter-organelle interactions result in a biochemical transformation of mitochondrial membranes and are required for functional in situ apoptotic pore formation.