The role of mantle–lithosphere interactions in shaping surface topography has long been debated1, 2, 3. In general3, 4, it is supposed that mantle plumes and vertical mantle flows result in axisymmetric, long-wavelength topography, which strongly differs from the generally asymmetric short-wavelength topography created by intraplate tectonic forces. However, identification of mantle-induced topography is difficult3, especially in the continents5. It can be argued therefore that complex brittle–ductile rheology and stratification of the continental lithosphere result in short-wavelength modulation and localization of deformation induced by mantle flow6. This deformation should also be affected by far-field stresses and, hence, interplay with the ‘tectonic’ topography (for example, in the ‘active/passive’ rifting scenario7, 8). Testing these ideas requires fully coupled three-dimensional numerical modelling of mantle–lithosphere interactions, which so far has not been possible owing to the conceptual and technical limitations of earlier approaches. Here we present new, ultra-high-resolution, three-dimensional numerical experiments on topography over mantle plumes, incorporating a weakly pre-stressed (ultra-slow spreading), rheologically realistic lithosphere. The results show complex surface evolution, which is very different from the smooth, radially symmetric patterns usually assumed as the canonical surface signature of mantle upwellings9. In particular, the topography exhibits strongly asymmetric, small-scale, three-dimensional features, which include narrow and wide rifts, flexural flank uplifts and fault structures. This suggests a dominant role for continental rheological structure and intra-plate stresses in controlling dynamic topography, mantle–lithosphere interactions, and continental break-up processes above mantle plumes.