The Pipe 200 kimberlite in northern Lesotho on the southeast margin of the Kaapvaal Craton is a diamond-poor deposit despite its proximity to economically viable kimberlites like the Liqhobong kimberlite. We study harzburgite xenoliths' mineral composition, geochemistry, and pressure–temperature evolution to understand factors influencing diamond destruction. The xenoliths are classified into five types based on their petrography and geochemistry. The diversity in the mineral assemblage correlates with a sampling depth of ~ 100 to 175 km (~ 2.8 to < 5.0 GPa). The signatures of metasomatism are evident in type 3 and 4 xenoliths, where garnet breaks down to form a cluster (henceforth assemblage) of phlogopite, chromite, and diopside. Fine-grained melts associated with an uplift in the mantle to shallower depths of < 90 km (< 2.3 GPa) encompass the minerals in the assemblage, which display resorption at the boundaries. Water contents (structural hydroxyl) of olivine and possibly orthopyroxene are lower in the xenoliths with metasomatism-induced breakdown of garnet. The structural hydroxyl distribution in the nominally anhydrous minerals shows flat distribution profiles of re-equilibration due to residence in the kimberlite magma. It is supported by the disruption of the inter-mineral water partition coefficient due to olivine water diffusion during residence in the kimberlite magma. The barren nature of the Pipe 200 kimberlite is attributed to the signatures of mantle metasomatism and residence in kimberlite magma, which led to the diamond destruction.