Abstract: Magnesium nanoparticles (NPs) with initial size in the 10-50 nmrange were synthesized by inert gas condensation under helium flow and deposited on room temperature substrates. The morphology and crystal structure of the NPs ensemble were investigated as a function of the deposition time by complementary electron microscopy techniques, including high resolution imaging and chemical mapping. With increasing amount of material, strong coarsening phenomena were observed at room temperature: small NPs disappeared while large faceted NPs developed, leading to a 5-fold increase of the average NPs size within a few minutes. The extent of coarsening and the final morphology depended also on the nature of the substrate. Furthermore, large single-crystal NPs were seen to arise from the self-organization of primary NPs units, providing a mechanism for crystal growth. The dynamics of the self-assembly process involves the basic steps of NPs sticking, diffusion on substrate, coordinated rotation and attachment/coalescence. Key features are the surface energy anisotropy, reflected by the faceted shape of the NPs, and the low melting point of the material. The observed phenomena have strong implications in relation to the synthesis and stability of nanostructures based on Mg or other elements with similar features.