Forming a good Ge/dielectric interface is important to improve the electron mobility of a Ge metal oxide semiconductor field-effect transistor. A thin yttrium germanate capping layer can improve the properties of the Ge/GeO2 system. We employ electronic structure calculations to investigate the effect of oxygen vacancies in yttrium-doped GeO2 and the yttrium germanates Y2Ge2O7 and Y2GeO5. The calculated densities of states indicate that dangling bonds from oxygen vacancies introduce in-gap states, but the system remains insulating. However, yttrium-doped GeO2 becomes metallic under oxygen deficiency. Y-doped GeO2, Y2Ge2O7 and Y2GeO5 are calculated to be oxygen substoichiometric under low Fermi energy conditions. The use of yttrium germanates is proposed as a way to effectively passivate the Ge/dielectric interface.