This paper aims to solve the longstanding debate on the origin of the Comoros volcanic archipelago (Mozambique Channel, Indian Ocean) concerning whether it represents a hotspot trail or a boundary between the Lwandle and Somalia plates in possible connection with the East African Rift System (EARS). To achieve this goal, we analyzed rock samples from recently discovered and previously uninvestigated volcanoes and edifices by means of geochemistry and geochronology. Major‐trace element analyses and radiometric dating ( ⁴⁰ Ar/ ³⁹ Ar, K‐Ar, and (U‐Th)/He) allow us to identify a widespread phase of Comorian volcanism initiated at 9–8 Ma, involving the Zélée, Geyser, and Leven banks, three atolls east of the Comoros. Another tectono‐magmatic phase initiated at 2.5 Ma led to a N‐S widening of seamount volcanism, and to the progressive development of en‐échelon NW‐SE structures. With this new addition of atolls and seamounts, the Comoros Archipelago becomes a ∼700 km‐long, ∼200 km‐wide E‐W chain extending from the Cenozoic volcanoes of Madagascar to the EARS. The reactivation of this chain at 9–8 and 2.5 Ma coincides with abrupt changes in the motion of the Somalia plate relative to the Lwandle plate, and with plate boundary modifications. The en‐échelon reorganization of structures also matches the kinematic evolution of Somalia relative to Lwandle, from transtension (>3 Ma) to pure dextral slip (≤3 Ma) in the northern Mozambique Channel. We conclude that the Madagascar‐Comoros volcanic chain is a branch of the EARS and a plate boundary, further strengthening the link between magmatism and the Rovuma‐Lwandle‐Somalia plate kinematics.