Borehole samples of carbonatites and phlogopite-pyroxenites from the Angico dos Dias (AdD) intrusive alkaline complex, State of Bahia, Brazil, have been investigated in terms of mineralogy, geochemistry and C-O-Sr-Nd isotopes. The AdD complex, of Early Proterozoic age (2 Ga), intrudes the northern side of the São Francisco Craton. Mineralogy and petrography indicate that the studied rocks only partially preserved their magmatic textural features owing to their metamorphic re-equilibration (greenschist facies). The REE contents and LREE/HREE ratios of the AdD carbonatites are very high (mean 39793718 ppm and La/Yb = 215323, respectively), as for most Precambrian magmatic carbonatites. The AdD carbonatites are also enriched in 18O (δ18O = 11.9 to 15.8‰), possibly due to secondary processes (e.g. metamorphism, alteration) whereas carbon isotopes are in the range of ‘primary carbonatites’ (δ13C = −5.7 to −7.1‰). Most of the initial 87Sr/86Sr and 143Nd/144Nd values of the studied carbonatites were not appreciably modified by secondary processes. Their εtSr and εtNd values (20.0 to 25 and 0.7 to −4.5, respectively) indicate enriched mantle sources very different from the ‘depleted’ ones related to many Precambrian carbonatites from North America (0.6–2.6 Ga) and Africa (0.5–2.0 Ga). The Early Proterozoic Sr-Nd isotopic signatures of the AdD carbonatites are similar to those of the Early Cretaceous carbonatites from the Paraná basin. The latter carbonatites show a great isotopic variability ranging from Bulk Earth to the related potassic magmatism from Asunción-Sapucai graben in the Eastern Paraguay (K-ASU magmatism: εtSr = 35 to 50 and εtNd = −12 to −20). The very similar isotopic compositions of Precambrian and post-Palaeozoic carbonatites worldwide indicate that the subcontinental mantle variability lasted for long periods of time and indicate a large-scale mantle heterogeneity.