Annexin-A5 (AnxA5) is a Ca2+-dependent phospholipid-binding protein associated with the regulation of intracellular Ca2+ homeostasis. However, the precise role of AnxA5 in controlling mitochondrial Ca2+ signaling remained elusive. Here, we introduce a novel function of AnxA5 in regulating mitochondrial Ca2+ signaling. Our investigation revealed that AnxA5 orchestrates intermembrane space (IMS) Ca2+ access capacity upon high Ca2+ elevations induced by ER Ca2+ release, leading to AnxA5 translocation to the outer mitochondrial membrane. Through close association with the voltage-dependent anion channel (VDAC1), AnxA5 regulates the Ca2+-permeable state of VDAC1. By modulating IMS Ca2+ signaling, AnxA5 actively shapes mitochondrial ultrastructure and influences the dynamicity of the mitochondrial Ca2+ uniporter. Furthermore, our findings regarding AnxA5's localization in the VDAC1 microenvironment reveal its protective role in regulating cell death by controlling VDAC1's oligomeric state triggered by cisplatin-induced apoptosis. Our study uncovers AnxA5 as a regulator of VDAC1 in physiological and pathological conditions.