Silica phases, SiOx forming at surfaces of various silicon crystals, e.g., Si wafers, nanowires, and nanoparticles via Si oxidation are key building blocks of diverse applications in the fields of electronics, medicine, and photonics for instance. The Si oxidation has been established to produce amorphous SiOx films, and the resulting oxide/silicon structures are prototypical junctions or contacts of amorphous and crystalline materials of which formation and properties have been extensively studied to understand and develop functionality of SiOx/Si in the applications. Here, observation of hitherto undiscovered phase of the SiOx/Si material, which is crystalline without traditional amorphous silica, is presented. The crystalline SiOx/Si structures are produced in vacuum environment via controlled oxidations of Si where O atoms are incorporated beneath the topmost Si layer. Concomitantly some Si atoms are detached from the crystal, and diffuse to the topmost surface, consistent with previous theoretical predictions, retaining still a pure Si‐surface type reconstruction and leading to a crystalline stack of Si/SiOx/Si. In addition to providing a well‐defined platform to studies of the SiOx/Si system, the found crystalline phase is also hypothesized to decrease amounts of disorder‐induced defects in the applications. Presented electrical characterization via carrier‐lifetime and capacitor measurements support the hypothesis.