We report the investigation of the formation phases of silicon nanostructures obtained from thermal annealing of hydrogenated amorphous silicon (a-Si:H)-based multilayers using in situ X-ray diffractometry, XRD. The multilayers composed of alternating layers of a-Si:H and silicon oxide were deposited on -oriented crystalline silicon substrates using a plasma-enhanced chemical vapor deposition. Our results indicate that crystallization only starts after hydrogen effusion at a 500 °C annealing temperature, independent of the a-Si:H sublayer thickness. Hydrogen effusion results in the reordering of the silicon structure from the tetragonal to the diamond structure, while the films maintain their amorphous medium-range order. The onset of crystallization and phase separation occur at different annealing temperatures depending on the a-Si:H sublayer thickness. The fraction of the crystallized nanostructure are found to also depend on the a-Si:H sublayer thickness. Phase separation and formation of silicon nanostructures is observed by the shift of the SiO stretching vibration to higher wave numbers in the Fourier transform infrared (FTIR) absorption spectra. The different crystallization phases as observed with in situ XRD will be corroborated by measurements from Raman and FTIR spectroscopies. The crystallite size obtained from XRD compares well with that obtained from transmission electron microscopy.