Germanium exhibits superior hole and electron mobility compared with silicon, making it a promising candidate for replacement of silicon in certain future CMOS applications. In such applications, achieving atomically clean Ge surfaces and the subsequent deposition of ultrathin passivation barriers without interfacial reaction are critical. In this study, we present in situ x-ray photoelectron spectroscopy (XPS) investigations of hydrocarbon removal from the Ge surface utilizing atomic oxygen at room temperature, as well as removal of hydrocarbons and of germanium oxide (GeO2) through atomic hydrogen treatment at 350 °C. Subsequently, atomic layer deposition (ALD) was used to create a protective layer of hexagonal boron nitride (h-BN) with an average thickness of 3 monolayers (ML). Tris(dimethylamino)borane and ammonia precursors were utilized at 450 °C for the deposition process. Intermittent in situ XPS analysis during ALD confirmed h-BN growth, stoichiometry, and the absence of interfacial reaction with Ge. XPS analysis after subsequent exposure of the Ge film with a h-BN overlayer of ∼9 Å average thickness to 7.2 × 104 l of atomic O (O3P) at room temperature yielded no evidence of Ge oxidation, with only the surface layer of the h-BN film exhibiting oxidation. These results present a practical and scalable route toward the preparation of clean Ge surfaces and subsequent deposition of protective, nanothin h-BN barriers for subsequent processing.