The formation of self-assembled quantum dots (QD) is of increasing interest for applications in optical, nanoelectronic, biological and quantum computing systems. From the perspective of fabrication technology, there are great advantages if the whole device can be made using a single Si substrate. Furthermore, GeSi is a model semiconductor system for fundamental studies of growth and material properties. In practice, as the MBE growth of heterostructures is inherently a non-equilibrium process, the formation of self-assembled nanostructures is both complex and sensitive to growth and overgrowth conditions. The morphology, structure and composition of QDs can all change during growth. It is therefore crucial to understand their structures at different stages of growth at the atomic scale. Here, the characterization of QD growth using high-resolution high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) imaging is presented. Both the formation of uncapped QDs and the effect of the encapsulation are investigated, and the morphological and compositional evolution of the QDs and wetting layers are observed directly at the atomic scale for the first time. During encapsulation, the Ge content in the centres of the QD remains unchanged, despite significant intermixing, lateral spreading and a laterally inhomogeneous Ge distribution inside the Ge QD. The initial non-uniform wetting layer for the uncapped Ge QD becomes uniform after encapsulation, and a 3-monolayer-thick core with ∼ 60% Ge content is formed in the 2 nm-thick wetting layer with an average Ge content of ∼ 30%. The results were obtained by direct analysis of the Z-contrast STEM imaging without involving complex image simulations.