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The northeastern Estonian Precambrian basement, encompassing the Tallinn, Alutaguse, and Jõhvi domains, forms part of the eastern sector of the Fennoscandian Shield. This crustal segment comprises Paleoproterozoic back-arc volcanic–sedimentary successions intruded by Svecofennian granitoids and metamorphosed to amphibolite–granulite facies. Its lithological architecture and metallogenic characteristics show strong affinities with established mineralised provinces of southern Finland and central Sweden, including the Orijärvi and Bergslagen districts.In this study, more than 500 historical drill cores, together with associated legacy geophysical datasets, were reanalysed to re-evaluate the mineral and critical-metal potential of the NE Estonian basement. Base- and precious-metal anomalies (Cu–Zn–Pb; Au–Ag–As–Sb) are spatially associated with magnetite-bearing and sulphide–graphite gneisses. High-resolution MSCL-XYZ scanning of archived drill cores further reveals a range of multi-element associations indicative of diverse mineral systems, including Ni–Co–Cr, Mo–W–Bi, Sn–Zn–Cd, Cu–Ni, Nb–Y–P, and Au–Ag–As–Sb–Bi–W–Se–Sn. These signatures delineate previously unrecognised prospective intervals across all three basement domains.A compositional geostatistical workflow was applied to historical whole-rock geochemical data to mitigate biases arising from heterogeneous sampling density and analytical variability. Exploratory analyses conducted on raw datasets were complemented by centred log-ratio (clr) transformation, which enhanced coherence in multivariate patterns. Clr-based spatial maps, principal component analysis, and heat-map visualisations significantly improved the reliability of regional-scale interpretations and reduced artefacts related to mismatched neighbouring datasets.Lithological descriptions from historical drilling, often incomplete or inconsistent, were reinterpreted using major-element geochemistry, while trace-element data were reassigned within a refined Tallinn–Alutaguse–Jõhvi basement framework. Integration of these geochemical reclassifications with gravity and magnetic data constrains subsurface architecture and strengthens correlations with mineral systems recognised in the southern Svecofennian domain and the Bergslagen province.Overall, the integrated geochemical, geostatistical, and geophysical approach provides an updated metallogenic framework for the NE Estonian basement and identifies new exploration targets for critical raw materials, supporting ongoing research within the Horizon Europe DEXPLORE programme.