Microlite and U-enriched microlite were found in eluvium close to highly weathered granitic pegmatites actively mined as a source of tantalum ore and situated within the ∼1000–900 Ma old Kibara belt unit, Numbi mining area, South Kivu province of the Democratic Republic of the Congo. Two examined pegmatites differ in their mineral assemblages and in the degree of fractionation: in the Mungwe pegmatite (lepidolite subtype) cassiterite > microlite-group minerals (microlite + U-enriched microlite) > columbite-group minerals (columbite–tantalite), wodginite + ferrotapiolite; at the Misumari II pegmatite (beryl-columbite subtype) microlite > cassiterite, columbite–tantalite + wodginite–ferrowodginite. Both pegmatites underwent deep tropical weathering; however, the degree of hydrothermal alteration of the (Nb,Ta)-oxide minerals is rather low. Fragments of primary microlite and U-enriched microlite (the latter present only at the Mungwe pegmatite) are mostly homogeneous and compositionally uniform; locally U-enriched microlite forms outer zones of the grains. Primary microlite from the less-fractionated Misumari II pegmatite is rather homogeneous and has Ta/(Ta + Nb) = 0.74–0.94 and higher Ti = 0.07–0.23 apfu at the B-site compared to the Mungwe pegmatite with similar Ta/(Ta + Nb) = 0.82–0.88 and low Ti. Microlite from Misumari II has higher contents of almost all trace elements (including REE) except for Li, Sb, and Pb. Primary microlite from both sites has Ca/Na close to 1, low A-site vacancy, and high F. Uranium-enriched microlite shows ≤0.29 apfu U, moderate A-site vacancy, and lower concentrations of F. Alteration of the U-poor microlite is very limited compared to the U-enriched microlite where radiation damage disrupted the mineral structure prior to the alteration. The altered microlite is depleted in Na and F and has high vacancy at the A-site, but the B-site population is almost identical to that of the primary microlite, as are the U concentrations. Such a composition is typical for secondary low-T alterations related to weathering. We demonstrate that the combined results from Automated Mineralogy, Electron Microprobe Analysis, and LA-ICP-MS techniques (along with the specific alteration features) can be successfully used to prove the provenance of tantalum ore by comparison with other localities where microlite is a major Ta-bearing mineral.