A major obstacle for transforming large-area molecular junctions into a viable technology is the deposition of a top, metallic contact over the self-assembled monolayer (SAM) without chemically damaging the molecules and preventing an interface-limited charge transport. Often a thin conducting layer is softly deposited over the SAM to protect it during the deposition of the metal electrode which requires conditions under which organic molecules are not stable. We report a new protective layer based on carbon paint which is highly conductive and has metallic-like behavior. Junctions made of SAMs of n-alkanethiolates supported by Au were characterized with both dc and ac techniques, revealing that carbon paint protective layers provide a solution to three well-known challenges in molecular junctions: series resistance of the leads, poor interface conductance, and low effective contact area related to the roughness of the interfaces. Transport is constant with coherent tunneling down to 10 K, indicating the carbon paint does not add spurious thermally activated components. The junctions have both high reproducibility and good stability against bias stressing. Finally, normalized differential conductance analysis of the tunneling characteristics of the junctions as a function of molecular length reveals that the scaling voltage changes with molecular length, indicating a significant voltage drop on the molecules rather than on the molecule–electrode interface. There is a clear inverse dependence of the scaling voltage on length, which we deduced has a tunneling barrier height of close to 2 eV. The paper establishes the reliability of carbon paint protective layers and provides a procedure for discriminating genuine molecular effects from interfacial contributions.