Marine sponges have emerged as major players within coral reef biogeochemical cycles, facilitating intake and release of carbon, nitrogen, and phosphorus. The majority of studies have investigated the role of sponges in transforming dissolved carbon and nitrogen; however, the same breadth of insights has not been extended to phosphorus. This study uses 32P-labeled orthophosphate and ATP to determine that two marine sponges, Lendenfeldia chondrodes and Hymeniacidon heliophila, both rapidly take up ambient dissolved inorganic phosphate and dissolved organic phosphorus. Subsequent genetic analysis and chemical extraction showed that sponge symbionts store phosphorus in the form of energy-rich polyphosphate (poly-P). L. chondrodes, a sponge from oligotrophic habitats and with a microbiome dominated by cyanobacterial symbionts, stores more phosphorus as poly-P (6–8%) than H. heliophila (0.55%), a eutrophic sponge with low cyanobacterial abundance. This work adds new insights to the roles of the sponge holobiont in cycling the crucial element, phosphorus.