Malate and fumarate constitute a significant fraction of the carbon fixed by photosynthesis, and they are at the crossroad of central metabolic pathways. In Arabidopsis thaliana, they are transiently stored in the vacuole to keep cytosolic homeostasis. The malate and fumarate transport systems of the vacuolar membrane are key players in the control of cell metabolism. Notably, the molecular identity of these transport systems remains mostly unresolved. We used a combination of imaging, electrophysiology and molecular physiology to identify an important molecular actor of dicarboxylic acid transport across the tonoplast. Here, we report the function of the A. thaliana Aluminium-Activated Malate Transporter 5 (AtALMT5). We characterised its ionic transport properties, expression pattern, localisation and function in vivo. We show that AtALMT5 is expressed in photosynthetically active tissues and localised in the tonoplast. Patch-clamp and in planta analyses demonstrated that AtALMT5 is an ion channel-mediating fumarate loading of the vacuole. We found in almt5 plants a reduced accumulation of fumarate in the leaves, in parallel with increased malate concentrations. These results identified AtALMT5 as an ion channel-mediating fumarate transport in the vacuoles of mesophyll cells and regulating the malate/fumarate balance in Arabidopsis.