<p>Self-template transformations are widely used for preparation of lanthanide (Ln³⁺) based nanoparticles with tunable porosity and composition, considering of their outstanding performance in optical, drug delivery and bio-imaging. However, it is still a major challenge to characterize the crystallization process, morphology and composition changes of these nanostructures in atomic scale and three-dimensional (3D). In this paper, we investigate the transformation of amorphous precursor to porous Y₂O₃:Eu³⁺ nanocrystals with advanced microscopy techniques. The morphology changes and compositions under different temperatures are identified through in-situ microscopy. The porous structures in 3D is clearly studied via electron tomography. Insights from this research are of broader interest for the class of transformation reactions, which will definitely shed light on the synthesis of complex nanostructures.</p> Graphical abstract <p>The transformation of amorphous precursor to porous Y₂O₃:Eu³⁺ nanocrystals was investigated via in-situ microscopy and electron tomography in 3D.</p>