Self-assembled monolayers of alkanethiolates on ferromagnetic metal surfaces have potential applications in molecular spintronics, but the fabrication of such structures is complicated by unwanted oxidation of the ferromagnetic metal. This paper describes the fabrication of ultra-smooth oxide-free Ni surfaces via template-stripping which are protected by SAMs of S(CH2)n−1CH3 that are stable for 1 day in ambient environment. Our method does not require ultra-high vacuum conditions, glove-box techniques, or (redox) cleaning of the Ni surface, but can be readily applied under ordinary laboratory conditions. Passivation of the Si/SiO2 template with a layer of FOTS (1H,1H,2H,2H-perfluorooctyltrichlorosilane) reduced the Ni-template interaction sufficiently enabling successful template-stripping. The NiTS–SAM interfaces were characterized by X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). We found that the surfaces were ultra-flat with a root mean square surface roughness of 0.15 ± 0.05 nm over 1.0 × 1.0 μm2 and that they were stable against oxidation for 1 day in air at room temperature. These SAMs on Ni were incorporated in SAM-based tunneling junctions of the form NiTS–SCn//GaOx/EGaIn to study the tunneling rate across the SAMs. The tunneling rate is highly sensitive to defects in the SAMs or the presences of oxides. We found that the charge transport properties across these junctions were indistinguishable from those junctions with formed on AuTS and AgTS substrates from which we conclude that our method yields high quality NiTS–SAM interfaces suitable for applications in molecular electronics.