The electronic structure of SiO2‐ versus Si3N4‐coated low nanoscale intrinsic silicon (Si) shifts away from versus toward the vacuum level Evac, originating from the Nanoscale Electronic Structure Shift Induced by Anions at Surfaces (NESSIAS). Using the quantum chemical properties of the elements involved to explain NESSIAS, an analytic parameter Λ is derived to predict the highest occupied energy level of Si nanocrystals (NCs) as verified by various hybrid‐density functional calculations and NC sizes. First experimental data of Si nanowells (NWells) embedded in SiO2 versus Si3N4 were measured by X‐ray absorption spectroscopy in total fluorescence yield mode (XAS‐TFY), complemented by ultraviolet photoelectron spectroscopy (UPS), characterizing their conduction band and valence band edge energies EC and EV, respectively. Scanning the valence band sub‐structure over NWell thickness yields an accurate estimate of EV shifted purely by spatial confinement, and thus the actual EV shift due to NESSIAS. Offsets of ΔEC = 0.56 eV and ΔEV = 0.89 eV were obtained for 1.9 nm thick NWells in SiO2 versus Si3N4, demonstrating an intrinsic Si type II homojunction. This p/n junction generated by NESSIAS eliminates any deteriorating impact of impurity dopants, offering undoped ultrasmall Si electronic devices with much reduced physical gate lengths and CMOS‐compatible materials.