The Earth’s crust beneath the Caribbean Sea formed at about 90 Ma due to large magmatic activity of a mantle plume, which brought molten material up from the deep Earth. By integrating diverse geophysical datasets, we image for the first time two fossil magmatic conduits beneath the Caribbean. The location of these conduits at 90 Ma does not correspond with the present-day Galápagos plume. Either this mantle plume migrated in time or these conduits were formed above another unknown plume.