Nanocrystals sometimes adopt unusual crystal structure configurations in order to maintain structural stability with increasingly large surface-to-volume ratios. The understanding of these transformations is of great scientific interest and represents an opportunity to achieve beneficial materials properties resulting from different crystal arrangements. Here, the phase transformation from α to β phases of tin (Sn) nanocrystals is investigated in nanocrystals with diameters ranging from 6.1 to 1.6 nm. Ultra-small Sn nanocrystals are achieved through our highly non-equilibrium plasma process operated at atmospheric pressures. Larger nanocrystals adopt the β-Sn tetragonal structure, while smaller nanocrystals show stability with the α-Sn diamond cubic structure. Synthesis at other conditions produce nanocrystals with mean diameters within the range 2–3 nm, which exhibit mixed phases. This work represents an important contribution to understand structural stability at the nanoscale and the possibility of achieving phases of relevance for many applications.