The aim of this research was to assess the ability of amalgam restorations to induce amorphous mineral precipitation at the caries-affected dentin substrate. Sound and caries-affected dentin surfaces were subjected to both Zn-free and Zn-containing dental amalgam restorations. Specimens were submitted to thermocycling (100,000 cycles/5°C–55°C, 3 months). Dentin surfaces were studied by atomic force microscopy (nanoroughness), X-ray diffraction, field emission scanning electron microscopy, and energy-dispersive analysis, for physical and morphological surface characterization. Zn-containing amalgam placement reduced crystallinity, crystallite size, and grain size of calcium phosphate crystallites at the dentin surface. Both microstrain and nanoroughness were augmented in caries-affected dentin restored with Zn-containing amalgams. Caries-affected dentin showed the shortest mineral crystallites (11.04 nm), when Zn-containing amalgams were used for restorations, probably leading to a decrease of mechanical properties which might favor crack propagation and deformation. Sound dentin restored with Zn-free amalgams exhibited a substantial increase in length of grain particles (12.44 nm) embedded into dentin crystallites. Zn-containing amalgam placement creates dentin mineralization and the resultant mineral was amorphous in nature. Amorphous calcium phosphate provides a local ion-rich environment, which is considered favorable for in situ generation of prenucleation clusters, promotong further dentin remineralization.