Quantum dots (QDs) have applications in optoelectronic devices, quantum information processing and energy harvesting. Although the droplet epitaxy fabrication method allows for a wide range of material combinations to be used, little is known about the growth mechanisms involved. Here we apply direct X-ray methods to derive sub-ångström resolution maps of QDs crystallized from indium droplets exposed to antimony, as well as their interface with a GaAs (100) substrate. We find that the QDs form coherently and extend a few unit cells below the substrate surface. This facilitates a droplet-substrate exchange of atoms, resulting in core-shell structures that contain a surprisingly small amount of In. The work provides the first atomic-scale mapping of the interface between epitaxial QDs and a substrate, and establishes the usefulness of X-ray phasing techniques for this and similar systems.