Abstract The destruction of the cratonic root has been documented for multiple cratons worldwide and is characterized by severe lithospheric thinning, extensive extensional deformation, and intense thermal activity. Here, we present detailed petrography accompanied by comprehensive geochemical and isotopic data for peridotites, pyroxenites, and eclogites from the SW margin of the São Francisco Craton that has also been severely thinned. The diamond-bearing Canastra-1 kimberlite represents a Cretaceous intrusion from the Alto Paranaíba Igneous Province and hosts garnet-bearing mantle xenoliths from different mantle sources, revealing a complex history of metasomatism/refertilization related to superimposed tectonic events since the cratonic consolidation. Eclogites (T = 978–982°C; P ~ 4.0 GPa) and pargasite-bearing websterites (T = 875–926°C; P = 2.0–3.0 GPa) represent the shallower and colder cratonic lithosphere. Mantle-derived high-MgO eclogitic clinopyroxenes show a light rare earth element (LREE)-enriched pattern (Ce/YbN = 60.90–93.63) while both clinopyroxene and garnet present high 87Sr/86Sr ratios (0.70842–0.70912) and negative εNd values (−5.6 to −7.3). These features, supported by the reconstructed whole-rock composition, suggest a mafic protolith probably metasomatized by fluid/melt derived from the overlying sedimentary rocks. Pargasite websterites are cumulates from an evolved (SiO2-rich) and hydrated basaltic andesitic magma. These xenoliths are characterized by high concentration of LREE relative to heavy-REE (HREE) in clinopyroxene (Ce/YbN = 10.52–50.61) and pargasite (Ce/YbN = 10.26–57.06), and by the presence of Al-rich orthopyroxene. As observed in eclogites, clinopyroxene and garnet from pargasite websterites display high 87Sr/86Sr ratios (0.70894–0.71094) and strong negative εNd values (−7.2 to −13.3). Trace elements (i.e. Zr, Ti, and Y) in garnets of both rock types indicate the role of a depleted component affected by a metasomatic agent. Although we were unable to date the formation of these rocks or the metasomatic events, we suggest a possible relationship with the consolidation of Gondwana during the Neoproterozoic. Sheared lherzolites, clinopyroxenites, anhydrous websterites, and dunite are deeper fragments from the lithosphere-asthenosphere boundary (LAB: 1191–1290°C; 5.3–5.6 GPa). They have abundant kelyphitic rims around garnet grains, which indicate metasomatism promoted by the percolation of a high-temperature proto-kimberlite melt enriched in Ti, Zr, and Y. The presence of kelyphitic phlogopite with high-Ti-Cr contents reinforces this assumption. LREE-enriched clinopyroxenes (Ce/YbN = 12.06–48.02) confirm the enriched character of the silicate melt responsible for the refertilization process within the cratonic root. The proto-kimberlite metasomatism is further supported by the preferential enrichment of 87Sr/86Sr ratios (0.70560–0.70869) accompanied by positive εNd values (+1.8 to +10.10). Two-point clinopyroxene-garnet Sm–Nd isochrons yielded an average age of 120 ± 5 Ma, representing the kimberlite eruption/emplacement age of the host kimberlite. These deeper LAB xenoliths reveal intense lithospheric thinning triggered by percolation of a high-temperature proto-kimberlite melt since the early stages of Gondwana break-up during the Cretaceous, shortly before the kimberlite emplacement at 120 Ma. Therefore, they provide remarkable evidence of the destruction of the São Francisco Craton through thermal-mechanical erosion that triggered its rejuvenation.