Mantle metasomatism by percolating melts/fluids can significantly modify the geochemical and mineralogical compositions of the sub-continental lithospheric mantle (SCLM). We present a detailed study of water contents and Li concentrations and isotopic compositions in mantle minerals from a suite of peridotite xenoliths entrained by a Cenozoic Strombolian volcano in the southern French Massif Central (FMC). Wide ranging clinopyroxene trace element distributions (e.g., (La/Yb)N from 0.25 to 22.21; Ti/Eu ratios from 453 to 4892) suggest that the SCLM has undergone metasomatism by carbonatitic melts/fluids or melts/fluids related to subducted materials. Two amphibole-bearing samples exhibit depletion of light rare earth elements (LREE; (La/Yb)N = 0.26 and 0.30, respectively) in amphiboles, similar to that in co-existing clinopyroxenes; these samples indicate that amphiboles grew during a separate modally metasomatic event predating the cryptic metasomatism accounting for LREE enrichment and negative HFSE anomalies in other samples. Mineral Li concentrations are similar to those in the normal mantle, with inter-mineral Li partitioning nearly equilibrated and intragranular Li distributions nearly homogeneous. However, negative δ7Li values of pyroxenes in some samples (as low as − 8.8‰ in clinopyroxene of sample MC38) can be attributed to diffusive exchange with a small-volume melt of moderate Li concentration and light Li isotopic composition, originally associated with a recycled component. Preservation of the currently observed large inter-mineral Li isotopic variations indicates that melt percolation occurred shortly before entrainment of the peridotite xenoliths by the host magma. Mineral water contents vary from 41 to 428 ppm in clinopyroxenes and from 28 to 152 ppm in orthopyroxenes, and their roughly negative co-variation with coexisting olivine Fo contents imply that partial melting was the main control over mineral water content variations in most samples. Varied water contents in LREE-enriched metasomatized samples indicate the involvement of metasomatic agents of different origins. The aqueous agent responsible for generation of amphiboles in two samples did not produce a notable increase in the water contents of coexisting nominally anhydrous minerals.