Broadband and long-period magnetotelluric soundings were collected along a 560 km E–W profile in a region of central Brazil subjected to Neoproterozoic collision tectonics and Archean to Cretaceous magmatic events. The profile crosses the northeastern portion of Phanerozoic sediments and volcanics of the Paraná basin, the southern extension of the Neoproterozoic metasedimentary rocks of the Brasília belt, locally pervaded by Cretaceous alkaline magmas of the Alto Paranaíba igneous province (APIP), and Neoproterozoic sedimentary cover and exposed Archean basement of the southern São Francisco craton. 2D conductivity structures derived by joint inversions of the TE and TM polarization modes and a separate inversion of the tipper components show signatures of the past tectonomagmatic events that affected the area. A gravity-defined suture zone beneath the Paraná basin is detected in the models as a subvertical conductor extending from crustal to upper mantle depths, which strengthen the interpretation of a Neoproterozoic collision of the São Francisco craton and a continental block beneath the sedimentary basin. Deep underthrusting of organic graphite-bearing metasedimentary rocks composing a fossil suture zone is proposed to explain such increase in electrical conductivity. A similar conductivity signature beneath the sedimentary covered region of the São Francisco craton can be tentatively interpreted as another similar cryptic suture zone. Other isolated high-conductivity anomalies at midcrustal depths below the Paraná and APIP provinces are interpreted as fossil residues representing precipitated graphite and sulfide derived from percolating volatiles during the emplacement of Cretaceous mafic-ultramafic volcanics. A very high conductivity wedge into the lower lithosphere is highlighted in the deep mantle beneath the APIP volcanic complex, coincident with a zone of low velocity defined by seismic tomography. Geochemical evidence indicates that the alkaline magmatism stemmed from a metasomatized upper mantle at only slightly raised temperatures. Thus, interconnected carbonatite melts of low melting point and graphite in the lithospheric mantle are the most likely candidates to explain this high conductivity. The seismic and conductivity anomalies are probably triggered by the same source mechanisms (incipient melting) because they are plausibly related to the same magmatic process. Conductivity anomalies at crustal and mantle depths in the southern segment of the São Francisco craton suggest that its lithosphere was significantly affected by the several tectonomagmatic episodes it has experienced throughout its geological history. Consequently, the enhanced conductivity in the lower crust can be genetically related to upwelling volatile-rich intrusions whereas upper mantle high conductivity can be related to refertilization by infiltrations of low-degree carbonatitic melts from deeper-sourced metasomatic processes.