Phosphorus (P) advanced treatment by adsorption reduces the risk of eutrophication in natural waters and reservoirs. The impact of ubiquitous Ca2+ on long-term P removal is critical in assessing the regeneration efficiency of one adsorbent, which is a vital indicator for cost-effectiveness. Given the critical role of lanthanum (La)-based composite materials in P removal, in this study, we unravel the long-term evolving role of Ca2+ on phosphate removal by nanosized hydrated lanthanum oxides (HLO) confined in cross-linked polystyrene beads (HLO@201) over 20 adsorption-regeneration cycles and fixed-bed column runs, with a combination of macroscopic adsorption experiments, microscopic structural investigation, and theoretical calculations. The role of Ca2+ gradually evolves from positive (5–70% higher than Ca2+-free group) to negative (18–41% lower than the Ca2+-free group) with ongoing cyclic runs of HLO@201, which is distinctive from the bulky HLO. The presence of Ca2+ enhances P uptake by HLO@201 possibly through ≡La–P–Ca–P multiple complexation and Ca–P precipitation (i.e., hydroxyapatite, HAP) inside the polymeric host, which creates an antagonistic effect with HLO over time. The formed Ca–P precipitates may accumulate and encapsulate on the surface of HLO nanoparticles, which induce the formation of irreversible LaPO4·xH2O under nanoconfinement that deplete the active adsorptive sites. A two-step (acid wash + NaOH) regeneration method can partially recover the P removal performance of HLO@201. We envision that this study could be a cautionary tale for advanced treatment of P by adsorption, to inspire re-evaluation on the long-term performance of adsorption processes.