Columnar microstructures are critical for obtaining good resistance switching properties in SiOx resistive random access memory (ReRAM) devices. In this work, the formation and structure of columnar boundaries are studied in sputtered SiOx layers. Using TEM measurements, we analyze SiOx layers in Me–SiOx–Mo heterostructures, where Me = Ti or Au/Ti. We show that the SiOx layers are templated by the Mo surface roughness, leading to the formation of columnar boundaries protruding from troughs at the SiOx/Mo interface. Electron energy-loss spectroscopy measurements show that these boundaries are best characterized as voids, which in turn facilitate Ti, Mo, and Au incorporation from the electrodes into SiOx. Density functional theory calculations of a simple model of the SiO2 grain boundary and column boundary show that O interstitials preferentially reside at the boundaries rather than in the SiO2 bulk. The results elucidate the nature of the SiOx microstructure and the complex interactions between the metal electrodes and the switching oxide, each of which is critically important for further materials engineering and the optimization of ReRAM devices.