The central part of the Karagwe-Ankole Belt (KAB) in the Great Lakes area of Central Africa is rich in various rare and strategic elements. The area north of Kalehe and Idjwi island within the Sud-Kivu Province of eastern Democratic Republic of the Congo (DRC) contains Nb, Ta, Sn and W mineralization hosted in pegmatites and quartz veins that are related to leucogranite intrusions. In this work, two granite-pegmatite fields were studied: the Bugarula field in the northern part of Idjwi island and the Kalehe field, along the west coast of Lake Kivu, with a view to determine the co-genetic link between different pegmatites and leucogranites in these regions. Based on mineralogical assemblages, five pegmatite zones were identified, occurring with some spatial overlap, but with an overall increasing distance from the inferred parental granite: 1) albite pegmatites, 2) two-mica pegmatites, 3) muscovite pegmatites, 4) beryl-bearing Nb–Ta–Sn mineralized pegmatites and 5) tourmaline-bearing Nb–Ta–Sn mineralized pegmatites. Muscovite compositions were analyzed from each zone and used to calculate pegmatite fractionation trends by using Rayleigh fractionation modelling. The model uses published partition coefficients (Kd) and measured contents of K, Rb and Cs in muscovite. Muscovites from the consecutive pegmatite zones in both the Bugarula and Kalehe pegmatite fields record a continuous fractionation trend, indicating a co-genetic magmatic evolution. A parental leucogranitic composition of 3.6 wt% K2O, 8 ppm Cs and 300 ppm Rb was iteratively determined to yield a best fit fractionation trend with the data. This composition is within the range of exposed leucogranites sampled in this study, which average at 4.2 wt% K2O, 7 ppm Cs and 400 ppm Rb (n = 12). It should be noted that individually, none of the sampled leucogranites gave satisfactory fractionation trajectories that would suggest a direct co-genetic link between them and the pegmatites. In the Idjwi granite-pegmatite field, the degree of fractionation with respect to the inferred parental leucogranite ranges from 20% to 99% for the least fractionated and most evolved Nb–Ta–Sn mineralized pegmatites, respectively. In the Kalehe area, fractionation values also range from 22% up to 99% for the least fractionated and most evolved (mineralized) pegmatites, respectively. Muscovites from mineralized pegmatites of zones 4 and 5 show high concentrations of Nb, Ta and Sn. As such, we show that muscovite compositions in these pegmatites provide a powerful tool to track Nb–Ta, Sn (and W) enrichment and potential mineralization. These high degrees of fractionation associated with the enrichment in economically interesting elements are similar to reported values for pegmatite fields elsewhere in the Karagwe-Ankole Belt.