In this work, we combine self-assembly and top-down methods to create hybrid junctions consisting of single organic molecular monolayers sandwiched between metal and/or single-crystalline semiconductor nanomembrane based electrodes. The fabrication process is fully integrative and produces a yield loss of less than 5% on-chip. The nanomembrane-based electrodes guarantee a soft yet robust contact to the molecules where the presence of pinholes and other defects becomes almost irrelevant. We also pioneer the fabrication and characterization of semiconductor/molecule/semiconductor tunneling heterojunctions which exhibit a double transition from direct tunneling to field emission and back to direct tunneling, a phenomenon which has not been reported previously.