Variations in the niobium/thorium ratio in basaltic rocks are thought to be related to the long-term extraction of continental crust from the mantle and the extent of sediment recycling and mixing in the mantle. However, basalts erupted between 13 and 3 Ma from a single volcanic center in the Cantal alkali massif (France) have Nb/Th of 10.5–18.7, a range encompassing nearly the entire basalt record. Cantal basalts are isotopically homogeneous, ruling out variable sediment contamination of their mantle sources. Instead, the new data indicate a mineralogical control on Nb/Th in a veined mantle source. We postulate that the large Nb/Th variations are the result of a metasomatic process, called percolative fractional crystallization, that produced veins containing pyroxene and Nb-rich oxide within the upper mantle. Short-term metasomatic-induced variations in mantle Nb/Th may have occurred throughout the geologic record, and provide an alternative explanation to sediment recycling for Nb/Th heterogeneity in the upper mantle.