Native oxides and associated residue are removed from surfaces of a substrate by sequentially performing two plasma cleaning processes on the substrate in a single processing chamber. The first plasma cleaning process removes native oxide formed on a substrate surface by generating a cleaning plasma from a mixture of ammonia (NH3) and nitrogen trifluoride (NF3) gases, condensing products of the cleaning plasma on the native oxide to form a thin film that contains ammonium hexafluorosilicate ((NH4)2SiF6), and subliming the thin film off of the substrate surface. The second plasma cleaning process removes remaining residues of the thin film by generating a second cleaning plasma from nitrogen trifluoride gas. Products of the second cleaning plasma react with a few angstroms of the bare silicon present on the surface, forming silicon tetrafluoride (SiF4) and lifting off residues of the thin film.