The western branch of the East African Rift hosts four main Neogene-Quaternary volcanic provinces, characterized by products with wide chemical and mineralogical variability. This study focuses on the two northernmost volcanic provinces, Toro Ankole where ∼0.2 Ma-old carbonatites, melilitites and kamafugites, erupted together with foidites, and Virunga where ∼13–9 Ma-old strongly and mildly alkaline rocks, from nephelinite up to trachytes crop out. Petrographic and whole/rock geochemical characteristics (low SiO2, high CaO and K2O, coupled with LILE enrichment) of 49 samples from Toro Ankole and 5 samples from Virunga (tephrites, trachybasalts and trachyandesites) point out enriched and heterogeneous sub-lithospheric mantle sources. The nature of the ultramafic nodules occasionally associated to the investigated samples highlights the presence of metasomatic veins variably enriched in clinopyroxene, phlogopite, carbonate, apatite, Ti-magnetite and titanite. 143Nd/144Nd ratios of Toro Ankole rocks are below ChUR (0.51249–0.51260), and all but two carbonatite lavas have 87Sr/86Sr ˃ BSE (0.7046–0.7056). Virunga lavas display less radiogenic 143Nd/144Nd (0.51235–0.51249) and more radiogenic 87Sr/86Sr ratios (0.7058–0.7071). Lead isotopes are all above the NHRL (206Pb/204Pb mostly in the range 19.12–19.63). δ11B values cover the whole OIB range (−8.3 to −3.3 ‰), but with the exception of some Toro Ankole samples with notably heavier compositions (−1.9 to 6.6), here linked to the carbonate enrichment. The differences in the isotopic features observed between Toro Ankole and Virunga products may reflect a north to south change of the lithospheric mantle source in terms of composition, mineralogy and depth of melting. Toro Ankole phlogopite-bearing mantle is more intensely metasomatized by a 87Sr- and 11B-rich component (as altered oceanic crust or subducted carbonates) compare to that one beneath Virunga, in which the metasomes might contain amphibole rather than phlogopite. Low degree of partial melting of the metasomatized mantle produces magmas of carbonatitic and ultrabasic/ultrapotassic compositions of the western rift branch.