Improvement in electrical properties of thermally grown GeO2/Ge metal-oxide-semiconductor (MOS) capacitors, such as significantly reduced flatband voltage (VFB) shift, small hysteresis, and minimized minority carrier response in capacitance-voltage (C-V) characteristics, has been demonstrated by in situ low temperature vacuum annealing prior to gate electrode deposition. Thermal desorption analysis has revealed that not only water but also hydrocarbons are easily infiltrated into GeO2 layers during air exposure and desorbed at around 300 °C, indicating that organic molecules within GeO2/Ge MOS structures are possible origins of electrical defects. The inversion capacitance, indicative of minority carrier generation, increases with air exposure time for Au/GeO2/Ge MOS capacitors, while maintaining an interface state density (Dit) of about a few 1011 cm−2 eV−1. Unusual increase in inversion capacitance was found to be suppressed by Al2O3 capping (Au/Al2O3/GeO2/Ge structures). This suggests that electrical defects induced outside the Au electrode by infiltrated molecules may enhance the minority carrier generation, and thus acting as a minority carrier source just like MOS field-effect transistors.