Due to their tunable current–voltage characteristics, Zn-doped thin SiO2 films are promising for microelectronic devices, e.g., memristors. In this work we studied single-crystal Si (100) substrates with 200 nm SiO2 surface layers implanted with 64Zn+ using Zn K-edge x-ray absorption spectroscopy (XAS), transmission electron microscopy (TEM) and electron diffraction. We used two specimens: as-implanted and annealed in oxygen at 700°C. Cross-section TEM analysis showed that 64Zn+ implantation leads to the formation of a subsurface layer consisting of Zn nanoparticles approximately 7 nm in size. The nanoparticles are distributed in depths from 10 nm to 90 nm, with a concentration peak at 45 nm. Electron microscopy showed that most of the Zn nanoparticles are amorphous. However, XAS data indicated that almost all the Zn atoms are coordinated with oxygen. Thus, only a small fraction of zinc atoms are involved in the formation of nanoclusters. Annealing at 700°C leads to the oxidation of particles with the formation of the Zn2SiO4 phase. The particle sizes in the surface layer of SiO2 after annealing vary from 3 nm to 20 nm.