The formation of magma chambers is a significant phase in the evolution of large oceanic intraplate volcanoes and has strong control on melt composition. There is, however, little information about the earliest magma chambers because the pre-shield stage of a volcano is difficult to access. Here we present thermobarometric data from embryonic seamounts near Madeira that provide us with the rare opportunity to sample the earliest stage of an oceanic island volcano. The erupted magmas indicate crystal fractionation in reservoirs ca. 500–1000 MPa (the upper 15–20 km of the mantle) and polybaric magma ascent including mixing events. Depths and degree of crystal fractionation during the pre-shield stage basically resemble the subaerial shield stage of Madeira. This contrasts with Pacific hotspot-islands such as Hawaii or Tahiti, where magma chambers of the pre-shield and shield stages are more distinct. We propose that the different manifestations of early hotspot volcanism are related to plate velocities controlling thermal gradients in the lithosphere. Because of slower plate velocity, the lithosphere is compositionally and thermally more uniform beneath Madeira than beneath Hawaii. This results in only minor rearrangements of the magma plumbing systems during evolution from the pre-shield to the shield stage.