Y2O3 thin films are deposited by ion beam sputtering on Si, SrTiO3 and MgO substrates. In order to obtain a better knowledge on the phase transition mechanisms in yttrium oxide, the effects of ion implantation have been studied as a function of the initial microstructure of thin films. The different microstructures for the as-deposited and implanted samples have been studied and characterized by means of X ray diffraction, High Resolution Transmission Electron Microscopy and Electron Energy Loss Spectroscopy and are compared to the cubic-C and monoclinic-B phase of Y2O3. The experimental results show clearly the presence of non-equilibrium phases in the implanted and non-implanted thin films. A particular attention is paid to the understanding of the relationship between the oxygen vacancy network organization, the stoichiometry and the formation mechanisms of these crystallographic phases.