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Semiconductor quantum dots (QDs) are nanostructures that can enhance the performance of electronic devices due to their 3D quantization. Typically, heterovalent impurities, or dopants, are added to semiconducting QDs to provide extra electrons and improve conductivity. Since each QD is expected to contain a few dopants, the extra electrons and their parent dopants have been difficult to locate. In this work, we investigate the spatial distribution of the extra electrons and their parent donors in epitaxial InAs/GaAs QDs using local-electrode atom-probe tomography and self-consistent Schrödinger–Poisson simulations in the effective mass approximation. Although dopants are provided in both layers, the ionized donors primarily reside outside of the QDs, providing extra electrons that are contained within the QDs. Indeed, due to the quantum confinement-induced enhancement of the donor ionization energy within the QDs, a lower fraction of dopants within the QDs are ionized. These findings suggest a pathway toward the development of 3D modulation-doped nanostructures.