The mechanisms to remove the native oxide layer on Ge(001) surfaces by an in situ hydrogen plasma inside an atomic layer deposition (ALD) reactor has been studied. A strong dependence of the reaction mechanism in the temperature range commonly employed by ALD has been identified through the combined analysis of atomic force microscopy, x-ray photoelectron and Raman spectroscopy. At low temperatures (e.g., 110 °C), the hydrogen plasma removed both Ge and O species from the native GeO2 layer, but also induced surface damage to Ge substrate. At high temperatures (e.g., 330 °C), only O species were removed from the native oxide leaving a nanocrystalline Ge overlayer behind. The thermodynamically unstable nature of hydrogen passivation on Ge resulted in a Ge surface with a high density of dangling bonds. The transition temperature between the two reaction mechanisms was determined to be about 270 °C, allowing to compromise between removing a native oxide layer entirely and hydrogenating the underlying Ge surface without surface damage.