Structural variations of SiOx matrix have been studied with Fourier Transform Infrared Spectroscopy (FTIR) during the formation of Si and Ge nanocrystal. Two frequently used methods, magnetron sputtering and ion implantation have been employed to form SiOx matrix containing excess Si and Ge. The Si-O-Si stretching mode has been deconvoluted to monitor the evolution of SiOx films during the annealing process. The integrated area and the shift in the SiOx peak positions are found to be well correlated with the change of the film stoichiometry and nanocrystal formation. It is shown that the nonstoichiometric SiOx matrix turns into stoichiometric SiO2 as the excess Si and Ge atoms precipitate to form nanocrystals. This process takes place at much lower temperatures for Ge than Si for both ion implantation and magnetron sputtering. FTIR technique is shown to be useful to study the matrix hosting nanocrystals to monitor nanocrystal formation.