The effects of ion irradiation on the microstructural evolution of sol-gel-derived silica-based thin films were examined by combining the results from Fourier transform infrared, Raman, and X-ray photoelectron spectroscopy, Rutherford backscattering spectrometry, and elastic recoil detection. Variations in the chemical composition, density, and structure of the constituent phases and interfaces were studied, and the results were used to propose a microstructural model for the irradiated films. It was discovered that the microstructure of the films after ion irradiation and decomposition of the starting organic materials consisted of isolated hydrogenated amorphous carbon clusters within an amorphous and carbon-incorporated silica network. A decrease in the bond angle of Si-O-Si bonds in amorphous silica network along with an increase in the concentration of carbon-rich SiOx C-y tetrahedra were the major structural changes caused by ion irradiation. In addition, hydrogen release from free carbon clusters was observed with increasing ion energy and fluence.