The aim of this study was to ascertain the crystal morphology and to assess the ultrastructure and texture changes of sound (SD) and caries-affected dentin (CAD) after being restored with Zn-free and Zn-containing amalgam. Dentin surfaces were studied before amalgam placement and after amalgam removal by X-ray diffraction (μXRD²) and transmission electron microscopy (TEM) through selected area diffraction (SAED) and bright-field (BF) imaging. Crystals at the dentin surface were identified as hydroxyl-apatite with augmented crystallographic maturity, crystallinity and grain sizes and lower microstrain in CAD dentin after Zn-containing amalgam removal at the 310 plane. The opposite trend was followed at 002 reflection. Texture increased in CAD at both reflections after the removal of Zn-containing amalgams. Crystallinity increased in SD after amalgam restorations at 002 and 310 reflections. In CAD, crystallinity decreased after amalgam restorations at the 002 plane. Block-like and needle-like apatite crystals constituted the bulk of minerals in SD. Needle-like apatite crystals were observed in CAD surfaces before and after Zn-free amalgam restorations. Polyhedral and rounded drop-like crystals characterized the CAD surfaces before Zn-containing amalgam placement. After the restoration removal, plate-like polygons and three-dimensional agglomerated crystals were revealed. Crystallites with improved crystallographic orientation became shorter and thinner in CAD treated with Zn-containing amalgams, thus increasing mineralization and maturity.