Using a semiconductor as the substrate to a molecular organic layer, penetration of metal contacts can be clearly identified by the study of electronic charge transport through the layer. A series of monolayers of saturated hydrocarbon molecules with varying lengths is assembled on Si or GaAs and the junctions resulting after further electronic contact is made by liquid Hg, indirect metal evaporation, and a “ready-made” metal pad are measured. In contrast to tunneling characteristics, which are ambiguous regarding contact penetration, the semiconductor surface barrier is very sensitive to any direct contact with a metal. With the organic monolayer intact, a metal–insulator–semiconductor (MIS) structure results. If metal penetrated the monolayer, the junction behaves as a metal–semiconductor (MS) structure. By comparing a molecule-free interface (MS junction) with a molecularly modified one (presumably MIS), possible metal penetration is identified. The major indicators are the semiconductor electronic transport barrier height, extracted from the junction transport characteristics, and the photovoltage. The approach does not require a series of different monolayers and data analysis is quite straightforward, helping to identify non-invasive ways to make electronic contact to soft matter.