This work provides a description, at the atomic level, of a mechanical treatment on a mixture composed of two metallic powders. We used Molecular Dynamics to simulate the impact of grinding balls involving compaction and plastic deformation. Four binary mixtures were considered: Ni-Al, Ti-Al, Fe-Ni, and Fe-Cr, in order to assess the influence of the mechanical and structural properties of these pure elements on the characteristics of the activated mixture. The formation of nanometric mixing zones was tracked over deformation steps. The microstructure of the activated mixture was characterized using various indicators: local crystallographic configuration, radial distribution function, potential energy distribution, and mixing efficiency. The effects induced by the mechanical treatment were found to be specific for each binary system, and depended on both the mechanical and structural properties of the pure elements. Mechanical activation induces solid-state solubility, structural transformations, and defects. We also evaluated reactivity and transport properties at different temperatures in Ni-Al and Ti-Al nanocomposites fabricated by mechanical activation. We assessed the extent of their mixing zones, together with solubility, mobility, and the formation of intermetallics within these zones.