Use of amorphous precursors is a widespread strategy in biomineralization. In sea urchin embryos, controlled transformation of amorphous calcium carbonate (ACC) to calcite results in smoothly curving and branching single crystals. However, the mechanism of the disorder-to-order transformation remains poorly understood. Here, the use of strontium as a probe in X-ray absorption spectroscopy (XAS) greatly facilitates investigation of the evolution of order. In pulse-chase experiments, embryos incorporate Sr2+ from Sr-enriched seawater into small volumes of the growing endoskeleton. During the chase, the Sr-labeled mineral matures under physiological conditions. Based on Sr K-edge spectra of cryo-frozen whole embryos, it is proposed that the transformation occurs in three stages. The initially deposited calcium carbonate has short-range order resembling synthetic hydrated ACC. Within 3 h, the short-range order of calcite is established. Between 3 h and 24 h, the short-range order does not change, while long-range order increases. These results refute the notion that organisms imprint the local order of the final crystal on ACC. Furthermore, it is proposed that the intermediate is more similar to disordered calcite than to anhydrous ACC. Pulse-chase experiments in conjunction with heavy element labeling have great potential to improve understanding of phase transformations during biomineralization.