The confinement of phosphates inside adsorbents is important for not only entrophication control, but also the recovery of phosphorous, a depleting natural resource. However, the behaviour of chemisorbed phosphates inside nanoporous materials has not been systematically studied. Here, the confinement of chemisorbed phosphates in a three-dimensional cubic mesoporous material with adjustable structural parameters is systematically investigated. By taking advantage of advanced electron tomography techniques, the relationship between the growth of chemisorbed phosphates, the overall phosphate-adsorption performance and the mesostructural parameters is revealed. Cubic cage-type FDU-12 materials with tuneable entrance sizes were prepared and functionalised with different amounts of lanthanum oxide. When the entrance size is smaller than approximately 5 nm, phosphates are found only in isolated cages, thereby leading to low lanthanum (La) usage efficiency and phosphate removal capacity. When the entrance size is increased, chemisorption occurs in both cages and entrances, thus forming crystalline LaPO4 nanorods and increasing both the La usage efficiency and the phosphate removal capacity. In addition, the LaPO4 nanorods show a preferential orientation along the  direction. This study provides new insights in the rational design of phosphate adsorbents with controlled structures and high performance.