Since 2018, the submarine east flank of Mayotte Island (Comoros archipelago) is the site of a major eruption located at 3.5 km depth bsl on a WNW-ESE volcanic ridge. Samples brought by oceanographic cruises carried out to monitor this seismo-volcanic crisis indicate that this volcanic ridge is built by a bimodal sodic alkaline magmatic series that includes basanites and phonolites. A petrological study of dredged samples allowed us to image the magmatic system feeding the volcanic ridge and to determine the link between basanitic and phonolitic magmas. The magmatic system feeding the volcanic ridge comprises multiple levels of magma storage. Basanitic magmas generated at 80–100 km mantle depth are stored in two or more deep reservoirs (≥ 37 km) and then in shallower basanitic and phonolitic lenses located close to the Moho interface before rising the surface. This study identifies three possible scenarios: (1) the deep basanitic magma rises directly and quickly to the surface from the deep mantle reservoir (as is currently happening 60 km offshore), (2) the basanitic magma stalls in a shallower reservoir near the Moho before resuming its ascent toward the surface and erupting as porphyritic basanite, (3) the basanitic magma stops and evolves to phonolite in these sub-crustal reservoirs. The phonolitic lavas are produced by approximately 80% fractional crystallization (34% clinopyroxene, 30% anorthoclase feldspar, 15.5% magnetite, 12.5% olivine, 5% apatite and 4% ilmenite) of a hydrous basanitic magma at mantle depths (P > 0.6 GPa) under reduced oxygen fugacity (~ FMQ-1). In this third scenario, the phonolitic magma might be reactivated by the arrival of a new batch of deeper basanitic magma.