<p>Marine phosphates, such as carbonate fluorapatite (CFA) and bioapatite, are rich in rare earth elements and yttrium (REY) are promising resources for our transition to a low-carbon emission future, but mechanisms controlling the enrichment of REY from seawater (∼10⁻⁵ ppm) to marine phosphates (&gt;1000 ppm) are poorly constrained. Here, we investigate an extraordinary REY-rich phosphorite from a central Pacific seamount, with REY concentrations reaching up to 1 wt.%. The CFA and foraminifer within the phosphorite yield a U-Pb age of ca. 55 Ma and negative carbon isotope excursion of ∼8‰, respectively, being coeval with the Paleocene-Eocene Thermal Maximum (PETM). Our results reveal that the REY enrichment in marine phosphates is paced with a sharp increase in productivity-related (e.g., Zn, Cu, and Fe) and redox-sensitive elements (e.g., U and Mo). We therefore propose that, during global warming periods (e.g., PETM), elevated marine primary productivity promoted the generation of abundant organic matter, which efficiently adsorbed REY during its settling. During subsequent degradation, REY were released from the organic matter and retained in pore water, effectively facilitating their transfer from surface seawater to deep-sea sediments and promoting the formation of REY-rich phosphates. This perspective underscores the critical role of an enhanced oceanic biogeochemical cycle in forming REY-rich marine phosphates and provides new insights into the marine geochemical cycles of P and REY under global warming conditions.</p>