The Mangodara district (southwestern of Burkina Faso, West African Craton) consists of a regional-scale Eburnean dome cored by granitoid-gneisses comprising rafts of migmatitic paragneisses and amphibolites of the Paleoproterozoic Birimian series. The occurrence of rare metal-bearing pegmatites in diffuse contact with these migmatitic and granitoid gneisses suggests that they originated from the segregation of a residual melt of these partially molten hosts. In this paper, we constrain the petrogenetic link between pegmatites and their hosts, and the mechanisms of rare metal fractionation in Lithium-Cesium-Tantalum (LCT) vs Niobium-Yttrium-Fluorine (NYF) petrogenetic signatures by the geochemistry of micas, apatite, columbite-group minerals, garnet, and zircon. Titanite-allanite pegmatites (containing titanite, allanite, epidote, zircon, and apatite as accessory minerals) and their evolved equivalent, apatite-zircon pegmatites (richer in apatite, lower K/Rb and Fe/Mn ratio in biotite but Li-depleted) are poorly mineralized metaluminous pegmatites. They display a continuous evolution trend in K/Rb and Fe/Mn in biotite and similar REE patterns in apatite, which favor an origin by segregation of residual melt within tonalitic-trondhjemitic gneiss in the core of the Mangodara dome. Garnet-columbite pegmatites containing REE-bearing phosphates and Zr-U-Th-bearing metamict minerals are mixed LCT + NYF pegmatites. Their micas, slightly enriched in Li, LREE-rich apatite, and Nb-Ta-U-rich garnet, are consistent with an origin by partial melting of a metasedimentary source, with dehydration of biotite (reservoir of Li, Rb, Nb) and dissolution of apatite-monazite (reservoir of REE). Apatite crystals in one garnet-columbite pegmatite reveal an inherited REE signature typical of apatite-zircon pegmatite, which suggests mingling of a LCT pegmatite-forming melt with the residual melt derived from crystallization of metaluminous pegmatites. Garnet-REE pegmatites, containing ilmenite-pyrophanite and euxenite-aeschynite), are NYF pegmatites that should originate from melt segregation within granodioritic gneiss associated with breakdown/entrainment of amphibole (reservoir of REE, Y) and LREE segregation by allanite and phosphates in the source. These data show that the LCT vs NYF signature of pegmatites of the Mangodara district results primarily from the chemical composition of the partially-molten source and the minerals involved in the partial melting reactions, which vary as a function of increasing depth (mica, phosphate, amphibole, garnet). The traceelement signature of anatectic peraluminous pegmatite-forming melt might then be affected by mingling with residual Nb-enriched metaluminous melt.