A new submarine volcano has been discovered offshore Mayotte, a part of the Comoros volcanic archipelago located between Africa and Madagascar. The edifice arose from the sea-floor following a seismo-volcanic crisis that started in May 2018. This seismo-volcanic activity highlights very deep magma reservoirs and dykes in the East Mayotte volcanic system. Since the crisis, the region has experienced >2000 earthquakes with magnitude ≥3.5 and activity continues today (August 17, 2021). The earthquakes are unusually deep and distributed into two swarms: one 5–15 km east of Petite-Terre at 25–55 km depth and a second 25 km away at 30–50 km depth. Significant subsidence of Mayotte to the East has been assigned to the drainage of a deep magma chamber, inferred to be located 30 km from the coast. However, at present, the earthquake locations and geodetic observations have not been sufficient to image entirely the structure of the volcanic plumbing system. In this study, we construct Vp, Vs, dVp, dVs and Vp/Vs 3D velocity models to assess the deeper structure of the young volcano plumbing system, offshore and East of Mayotte. Using >3000 earthquakes from an ongoing monitoring effort, and a 1D velocity model determined onboard, we jointly inverted for velocity structures, earthquake locations, origin times, and station corrections using LOTOS software. The calculated 3D velocity models highlight a complex volcanic system down to 40 km depth. Specifically, we image 3 interpreted reservoirs, more or less consolidated/old. The main reservoir is located at about 30 km depth and deeper, making it one of the deepest magmatic chamber imaged. The reservoirs are connected by several old crystallized conduits, whose existence could have been influenced by the presence of an old fracture zone, globally oriented N130°, due to a regional strike-slip motion of the lithosphere. Moreover, gas-saturated rock may be present below the currently degassing Horse Shoe structure. We were unable to image connections between the new volcanic edifice and reservoirs or conduits due to a lack of resolution in that part of the study area.