SUMMARY A large-scale magnetotelluric (MT) study was carried out in offshore Borneo to understand the lithospheric structure in this geologically complex region where three tectonic plates converge and past crustal studies generated long-standing debates. Marine MT data were acquired at 1416 stations with 3 km spacing along 13 regional lines (covering 4677 line-km) with periodicities of 0.1 to 10 000 s. These were inverted in 3-D incorporating electrical anisotropy with cross-gradients constraints between vertical and horizontal resistivities and the results were validated with resistivity well-logs from several exploration wells. The models reveal widespread presence of electrically resistive upper crustal and uppermost mantle layers, each underlain by a laterally varying conductive and anisotropic layer. The geometries of the anisotropic layers suggest large-scale ductile flow, thrusting and folding forming belts of alternating deep roots and thin lithosphere, consistent with multiple underthrusting/subduction. Our results are in agreement with the seismologically detected lithospheric variations in northern Borneo suggesting onshore–offshore continuity and a common lithospheric–asthenospheric origin for the deformation patterns. Over thinned lithosphere, we found consistent low resistivity and high anisotropy anomalies in the mantle above the spatial locations of fast shear-wave bodies imaged by recent seismological workers which we interpret to indicate post-subduction lithospheric–asthenospheric ductile flow in response to multidirectional regional compression. We demonstrate that these zones are spatially correlated with the distribution of mainly Cretaceous ophiolitic rocks and melanges exposed onshore and suggest that serpentinization of mantle peridotite can explain some of the anisotropic conductivity anomalies. The taper zones of these deep anisotropic conductors are also associated with Neogene sub-basins, high thermal gradients, and intrasedimentary magmatic bodies indicating a link between lithospheric thinning and magmatism. We propose that such anomalies could be important pathfinders for geothermal and natural hydrogen systems in the ongoing global drive for carbon-free energy resources.