Mantle exhumation at slow-spreading ridges is favoured by extensional tectonics through low-angle detachment faults1, 2, 3, 4, and, along transforms, by transtension due to changes in ridge/transform geometry5, 6. Less common, exhumation by compressive stresses has been proposed for the large-offset transforms of the equatorial Atlantic7, 8. Here we show, using high-resolution bathymetry, seismic and gravity data, that the northern transform fault of the St Paul system has been controlled by compressive deformation since ~10 million years ago. The long-lived transpression resulted from ridge overlap due to the propagation of the northern Mid-Atlantic Ridge segment into the transform domain, which induced the migration and segmentation of the transform fault creating restraining stepovers. An anticlockwise change in plate motion at ~11 million years ago5 initially favoured extension in the left-stepping transform, triggering the formation of a transverse ridge, later uplifted through transpression, forming the St Peter and St Paul islets. Enhanced melt supply at the ridge axis due to the nearby Sierra Leone thermo chemical anomaly9 is responsible for the robust response of the northern Mid-Atlantic Ridge segment to the kinematic change. The long-lived process at the origin of the compressive stresses is directly linked to the nature of the underlying mantle and not to a change in the far-field stress regime.