We shed light on the nature and structure of the crust surrounding the Comoros Archipelago, western Indian Ocean, offering insights into the region's geological history and volcanic island formation. Our comprehensive study encompasses the acquisition of new, deeply penetrating seismic data from the SISMAORE cruise (refraction and reflection seismic), and the subsequent analysis of the characteristics and structure of the crust surrounding the Comoros Archipelago. Both the reflection seismic imaging and the velocity structure using ocean bottom seismometers indicate that the crust of the Comoros Basin exhibits oceanic characteristics, thus resolving previous controversies about its nature. The thickness of the oceanic crust ranges from 5.8 to 6.6 km in the north of the archipelago to 6–7.2 km within the Comoros Basin. The estimated roughness of the top basement in the Comoros Basin ranges from 110 to 200 m values typical of intermediate to slow spreading ridges, such as the extinct spreading centre in the West Somali Basin. The unloaded basement depth of the Comoros Basin closely matches the expected water-loaded subsidence for a Cretaceous or Jurassic oceanic lithosphere. In contrast, the West Somali Basin to the north of the Comoros Archipelago has shallower basement depths, potentially linked to recent volcanic activity along the archipelago. We propose that the pre-existing oceanic fracture zones in the West Somali Basin underwent reactivation, first during the Turonian period and later during the Late Eocene. These reactivated fracture zones may have acted as preferred pathways for the emplacement of the volcanic islands of the Comoros Archipelago. The EW trend of the archipelago appears to follow a marked change in the direction of these reactivated fracture zones, suggesting that the associated lithospheric weakening likely played a critical role in facilitating the formation of the Comoros Archipelago.