jats:titleAbstract</jats:title>jats:pWe present the first continental‐scale seismic model of the lithosphere and underlying mantle beneath Southeast Asia obtained from adjoint waveform tomography (often referred to as full‐waveform inversion or FWI), using seismic data filtered at periods from 20 to 150 s. Based on >3,000 hr of analyzed waveform data gathered from ∼13,000 unique source‐receiver pairs, we image isotropicjats:italicP</jats:italic>‐wave velocity, radially anisotropicjats:italicS</jats:italic>‐wave velocity and density via an iterative non‐linear inversion that begins from a 1‐D reference model. At each iteration, the full 3‐D wavefield is determined through an anelastic Earth, accommodating effects of topography, bathymetry and ocean load. Our data selection aims to maximize sensitivity to deep structure by accounting for body wave arrivals separately.jats:italicSASSY21</jats:italic>, our final model after 87 iterations across seven period bands, is able to explain true‐amplitude data from events and receivers not included in the inversion. The trade‐off between inversion parameters is estimated through an analysis of the Hessian‐vector product.jats:italicSASSY21</jats:italic>reveals detailed anomalies down to the mantle transition zone, including multiple subduction zones. The most prominent feature is the (Indo‐)Australian plate descending beneath Indonesia, which is imaged as one continuous slab along the 180° curvature of the Banda Arc. The tomography confirms the existence of a hole in the slab beneath Mount Tambora and locates a highjats:italicS</jats:italic>‐wave velocity zone beneath northern Borneo that may be associated with subduction termination in the mid‐late Miocene. A previously undiscovered feature beneath the east coast of Borneo is also revealed, which may be a signature of post‐subduction processes, delamination or underthrusting from the formation of Sulawesi.</jats:p>