While the “clean-up” effect on III-V substrates has recently been well documented interfacial reactions during atomic layer deposition (ALD) on Ge substrates are not fully explored. The “clean-up” of Ge oxides is studied by interrupting the ALD process following individual precursor pulses for in situ monochromatic x-ray photoelectron spectroscopy analysis. Germanium oxides are found to be reduced by TMA and water, while an interfacial GeON layer is only affected by the initial TMA pulse. Oxide free germanium surfaces behave analogously to a surface with initial native oxides since they are oxidized measurably prior to the first TMA pulse due to residual oxidants in a commercial ALD chamber.