Carbonatites are mantle-derived rocks associated with rare earth element deposits and their origin is debated. The majority of carbonatites are found in proximity to old continental crust and generally exhibit more geochemically enriched Sr and Nd isotopes relative to the prevalent mantle, with only a few known carbonatite occurrences found in intra-oceanic settings such as that in Cape Verde and Canary Island in the Atlantic Ocean. These oceanic carbonatites are moderately depleted with isotopic signatures similar to the prevalent mantle, indicating that Sr and Nd isotopic enrichment observed in continental carbonatites is controlled by the continental lithospheric mantle, metasomatized by melts and fluid over billions of years. Here we report a newly discovered intra-oceanic dolomite tuff unit with carbonatitic affinity, from the Kerguelen Archipelago, the emerged part of the long-lived Cretaceous Kerguelen Plateau. The Kerguelen dolomite tuff erupted at 24.1 ± 0.4 Ma after the main building phase of the northern Kerguelen Plateau and was fed by the Kerguelen mantle plume. The dolomite tuff shows strong Sr and Nd isotopic enrichments consistent with the presence of recycled material in the deep mantle source of the Kerguelen plume, possibly enriched during the assembly and breakup of the supercontinent Pangaea. These new data show a significant role of geodynamic processes in controlling deep material recycling, location of mantle plumes, and composition of carbonatitic melt.