Volcanic eruptions shape Earth’s surface and provide a window into deep Earth processes. How the primary asthenospheric melts form, pond and ascend through the lithosphere is, however, still poorly understood. Since 10 May 2018, magmatic activity has occurred offshore eastern Mayotte (North Mozambique channel), associated with large surface displacements, very-low-frequency earthquakes and exceptionally deep earthquake swarms. Here we present geophysical and marine data from the MAYOBS1 cruise, which reveal that by May 2019, this activity formed an 820-m-tall, ~5 km³ volcanic edifice on the seafloor. This is the largest active submarine eruption ever documented. Seismic and deformation data indicate that deep (>55 km depth) magma reservoirs were rapidly drained through dykes that intruded the entire lithosphere and that pre-existing subvertical faults in the mantle were reactivated beneath an ancient caldera structure. We locate the new volcanic edifice at the tip of a 50-km-long ridge composed of many other recent edifices and lava flows. This volcanic ridge is an extensional feature inside a wide transtensional boundary that transfers strain between the East African and Madagascar rifts. We propose that the massive eruption originated from hot asthenosphere at the base of a thick, old, damaged lithosphere.