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The thermochemical structure of the subcontinental mantle holds information on its origin and evolution that can inform energy and mineral exploration strategies, natural hazard mitigation and evolutionary models of the Earth. However, imaging the fine-scale thermochemical structure of continental lithosphere remains a major challenge. Here we combine multiple land and satellite datasets via thermodynamically-constrained inversions to obtain a high-resolution thermochemical model of central and southern Africa. Results reveal diverse structures and compositions for cratons, indicating distinct evolutions and responses to geodynamic processes. While much of the Kaapvaal lithosphere retained its cratonic features, the western Angolan-Kasai shield and the Rehoboth block have lost their cratonic keels. The lithosphere of the Congo Craton has been affected by metasomatism, increasing its density and inducing its conspicuous low-topography, geoid and magnetic anomalies. Our results reconcile mantle structure with the causes and location of volcanism within and around the Tanzanian Craton, whereas the absence of volcanism towards the north is the result of local asthenospheric downwellings, not to a previously-proposed lithospheric root connecting with the Congo Craton. Our study offers improved integration of mantle structure, magmatism and the evolution and destruction of cratonic lithosphere and lays the groundwork for futurelithospheric evolutionary models and exploration frameworks for the Earth and otherterrestrial planets.