n-Si/CnH2n + 1/Hg junctions (n = 12, 14, 16 and 18) can be prepared with sufficient quality to assure that the transport characteristics are not anymore dominated by defects in the molecular monolayers. With such organic monolayers we can, using electron, UV and X-ray irradiation, alter the charge transport through the molecular junctions on n- as well as on p-type Si. Remarkably, the quality of the self-assembled molecular monolayers following irradiation remains sufficiently high to provide the same very good protection of Si from oxidation in ambient atmosphere as provided by the pristine films. Combining spectroscopic (UV photoemission spectroscopy (UPS), X-ray photoelectron spectroscopy (XPS), Auger, near edge-X-ray absorption fine structure (NEXAFS)) and electrical transport measurements, we show that irradiation induces defects in the alkyl films, most likely CC bonds and CC crosslinks, and that the density of defects can be controlled by irradiation dose. These altered intra- and intermolecular bonds introduce new electronic states in the highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gap of the alkyl chains and, in the process, dope the organic film. We demonstrate an enhancement of 1–2 orders of magnitude in current. This change is clearly distinguishable from the previous observed difference between transport through high quality and defective monolayers. A detailed analysis of the electrical transport at different temperatures shows that the dopants modify the transport mechanism from tunnelling to hopping. This study suggests a way to extend significantly the use of monolayers in molecular electronics.