Nominally anhydrous mantle minerals (olivine, pyroxenes, garnets, etc.) in 11 peridotite xenoliths from four different uneconomic and economic Kaapvaal Craton kimberlite pipes (Matsoku, Thaba Putsoa, Pipe 200 and Bultfontein) have been investigated using Fourier transform infrared spectroscopy (FTIR). All xenoliths contain accessories of garnet, diopside, chromite, and phlogopite. High orthopyroxene content (>30 mol vol.%) in most xenoliths from all kimberlites and its interconnected channel-like nature hint towards hydrous siliceous fluid metasomatism. Peridotite xenoliths from uneconomic kimberlites show development of phlogopite and clinopyroxene (± chromite) forming veins and in garnet rims suggesting metasomatism by alkaline silico-carbonatite (possibly kimberlite-related) melt. The xenoliths contain significant H2O in olivine (17–62 ppm), orthopyroxene (21–230 ppm), and clinopyroxene (87–833 ppm), whereas garnets are dry and only show IR absorbance bands at > 3,670 cm−1 for contamination of hydrous minerals. Compared to the economic kimberlites in the Kaapvaal Craton, the uneconomic kimberlite xenoliths from this study have lower orthopyroxene and olivine H2O content. In the xenoliths affected by garnet breakdown metasomatism, the H2O content of orthopyroxene and olivine is higher and lower, respectively. The structural hydroxyl distribution profile across olivine and higher inter-mineral water partition coefficient, suggest diffusion of hydrogen and possible re-equilibration. Statistical analysis of the olivine spectra suggests that hydrogen bands at 3540, 3624, 3638, and 3672 cm−1 are a good discriminant of economic and uneconomic kimberlites and in literature, they are associated with metasomatism, weathering-associated processes, high water activity, and oxygen fugacity. The lower water concentration in xenoliths from uneconomic kimberlite from the margin of the craton than the economic kimberlites from the interior of the Kaapvaal Craton and identified metasomatism hints towards dehydration of xenoliths by water-poor and CO2-rich melts in tectonized cross-lithospheric zones causing diamond resorption and may be responsible for the diamond-poor nature of uneconomic kimberlites in northern Lesotho.