<p>Upper-plate rigidity plays a major role in controlling subduction-zone earthquake dynamics^1–3. However, its three-dimensional variability, particularly at the base of the upper plate, where most coseismic energy is released during rupture, remains poorly constrained globally. Here, we use 3D travel-time tomography from controlled-source seismic data to constrain the P-wave velocity distribution and interplate relief across the seismogenic zone of the North Ecuador-South Colombia margin. Velocity-derived rigidity reveals a complex 3D distribution above the interplate boundary. While the down-dip distribution follows well-documented global patterns, notable along-strike variations are observed within the rupture zones of major regional earthquakes (M_w &gt; 7). These variations occur across a smooth interplate boundary without major subducting topography and are controlled by crustal-scale faulting that forms localized low-rigidity upper-plate regions connected to the interplate. This elastic structure helps explain differences in the dynamics of past ruptures, providing insights into the seismogenic behaviour of the region.</p>