The Skyrme-particle, the skyrmion, was introduced over half a century ago in the context of dense nuclear matter. But with skyrmions being mathematical objects -special types of topological solitons -they can emerge in much broader contexts. Recently skyrmions were observed in helimagnets, forming nanoscale spin-textures. Extending over length scales much larger than the interatomic spacing, they behave as large, classical objects, yet deep inside they are of quantum nature. Penetrating into their microscopic roots requires a multi-scale approach, spanning the full quantum to classical domain. Here, we achieve this for the first time in the skyrmionic Mott insulator Cu 2 OSeO 3. We show that its magnetic building blocks are strongly fluctuating Cu 4 tetrahedra, spawning a continuum theory that culminates in 51a ‰nm large skyrmions, in striking agreement with experiment. One of the further predictions that ensues is the temperature-dependent decay of skyrmions into half-skyrmions. & copy; 2014 Macmillan Publishers Limited. All rights reserved.