AbstractThe Java ‐ Lesser Sunda margin, which features multi‐scale subducting oceanic basement relief, is classified as neutral (Lombok and Sumbawa) to erosional (Central Java to Bali) in comparison to its accretionary counterpart offshore Sumatra. However, a comprehensive analysis of how plate boundary and upper plate structure across the neutral to erosional transition are modulated by the subduction of oceanic basement relief is lacking to date. To shed light on the tectonic parameters that push the margin into the neutral or erosional domain, we combine multi‐channel reflection seismic images derived through a grid‐based P‐wave velocity inversion, and multibeam bathymetric maps. The data document how different scales of subducting topography modify seafloor morphology, upper plate structure, and décollement position. Large‐scale subducting features cause a landward shift of the deformation front, shortening of the accretionary wedge, and seafloor steepening at the relief's trailing edge. Small‐scale subducting ridges primarily impact the frontal prism resulting in over‐steepening at the trench and localized slope failure. Ahead of subducting relief, deformation of the accretionary wedge encompasses enhanced compression and a reduction in seafloor slope but appears independent of the size of the relief. Ridge and seamount subduction induce frontal erosion and basal erosion offshore Lombok and Bali, respectively. Our P‐wave velocity models indicate that the rigidity of the upper plate's base along the eastern Sunda margin is significantly lower than the worldwide trend. We conclude that this favors the genesis of tsunami earthquakes that have occurred on the Java margin.