Deep-sea sediments rich in rare-earth elements and yttrium (REY) have gained worldwide interest because of the increasing demand for REY in green-energy technologies, aiming to establish a carbon-neutral future. Bioapatite fossils (Ca5(PO4)3-x(CO3)xF1+x) are regarded as the main REY host in marine deposits, however, their quantity is disproportionally low compared to the abundance of phosphorous and REY in deep-sea sediments. Here, we report novel pellets of abiotic authigenic carbonate fluorapatite (AA-CFA) that contain over ~23,000 μg/g REY, thus serving as another significant REY host in deep-sea sediments. We show that phosphorous likely originates from P-bound hydrothermal Fe (oxyhydr)oxides, and that AA-CFA is a previously overlooked P sink in open ocean settings. We also show that AA-CFA pellets can record and preserve the neodymium (Nd) isotopic composition of bottom seawater. Altogether, the findings reshape our understanding of deep-sea REY deposits and P cycling, and highlight the potential of AA-CFA pellets as a new proxy for tracing water mass circulation.