The Kédougou-Kéniéba Inlier (KKI) corresponds to a window through Paleoproterozoic terranes of the West African Craton (WAC). This study presents, first of all, an interpretation of a regional Bouguer gravity map (14°W-9°W, 11°N-16°N) of the KKI and then introduces a new litho-structural map of the Malian part of the KKI using aeromagnetic data (12°0′W-10°80′W, 12°0′N-14°50′N). The KKI is limited to the west by a negative gravity anomaly forming a 30–100 km wide corridor, oriented N–S to NNE-SSW, and correlated to the Variscan Mauritanides orogenic belt. West of this belt, the Mesozoic to Cenozoic sedimentary deposits are marked by the highest positive anomaly of the region, attributed either to the presence of mafic rocks at intermediate to deep crustal levels or to a shallower Moho depth. Within the KKI, moderately positive to negative anomalies are correlated with exposed plutonic and mafic to intermediate metavolcanic rocks. Gravity data also reveal (i) two north-west trending lineaments attributed to crustal-scale shear zones, (ii) three north-east trending lineaments marked by gravity anomalies sub-parallel to the known Bissau–Kidira–Kayes Fault Zone, and named Kayes, Kédougou-Kéniéba, and South Shear Zones, respectively, (iii) and the extension to the south of the known Mauritanides Belt Thrust. The local aeromagnetic map of the Malian part of the KKI discriminates the Mako metavolcanic belt with granitic intrusions in the west characterized by heterogeneous anomalies, from the Kofi metasedimentary series delineated by magnetic lows in the east. ESE-WNW to ENE-WSW-trending alternation of magnetic anomalies in the metavolcanic and metasedimentary rocks are attributed to pervasive structures associated with ductile deformation. The Senegalo-Malian Shear Zone is marked at the regional scale by deflection of the geophysical lineaments but is not expressed by any offset of identified structures or lithological contacts.