The 500,000 km2 Saharan Metacraton in northern Africa (metacraton refers to a craton that has been mobilized during an orogenic event but that is still recognisable through its rheological, geochronological and isotopic characteristics) is an Archean Paleoproterozoic cratonic lithosphere that has been destabilized during the Neoproterozoic. It extends from the Arabian Nubian Shield in the east to the Trans- Saharan Belt in the west, and from the Oubanguides Orogenic Belt in the south to the Phanerozoic cover of North Africa. Here, we show that there are high S-wave velocity anomalies in the upper 100 km of the mantle beneath the metacraton typical of cratonic lithosphere, but that the S-wave velocity anomalies in the 175 250 km depth are much lower than those typical of other cratons. Cratons have possitive S-wave velocity anomalies throughout the uppermost 250 km reflecting the presence of well-developed cratonic root. The anomalous upper mantle structure of the Saharan Metacraton might be due to partial loss of its cratonic root. Possible causes of such modification include mantle delamination or convective removal of the cratonic root during the Neoproterozoic due to collision-related deformation. Partial loss of the cratonic root resulted in regional destabilization, most notably in the form of emplacement of high-K calc-alkaline granitoids. We hope that this work will stimulate future multi-national research to better understand this part of the African Precambrian. Specifically, we call for efforts to conduct systematic geochronological, geochemical, and isotopic sampling, deploy a reasonably-dense seismic broadband seismic network, and conduct systematic mantle xenoliths studies.