The thermochemical structure of the lithosphere controls melting mechanisms in the mantle, as well as the location of volcanism and ore deposits. Obtaining reliable images of the lithosphere structure, and its complex interactions with the asthenosphere, requires the joint inversion of multiple data sets and their associated uncertainties. In particular, the combination of seismic velocity and electrical conductivity, along with proxies for bulk composition and elusive minor phases, represents a crucial step toward fully understanding large‐scale lithospheric structure and melting processes. We apply a novel probabilistic approach for joint inversions of 3D magnetotelluric and seismic data to image the lithosphere beneath southeast Australia. The results show a highly heterogeneous lithosphere with deep conductivity anomalies that correlate with the location of Cenozoic volcanism. In regions where the conductivities have been at odds with sub‐lithospheric temperatures and seismic velocities, we observe that the joint inversion provides conductivity values consistent with other observations. The results reveal a strong relationship between metasomatized regions in the mantle and (a) boundaries of geological provinces, elucidating the subduction‐accretion process in the region; (b) distribution of leucitite and basaltic magmatism; (c) independent geochemical data, and (d) a series of lithospheric steps which constitute areas prone to generating small‐scale instabilities in the asthenosphere. This scenario suggests that shear‐driven upwelling and edge‐driven convection are the primary mechanisms for melting in eastern Australia, contrary to the conventional notion of mantle plume activity. Our study presents an integrated lithospheric model for southeastern Australia and provides valuable insight into the mechanisms driving surface geological processes.