Electrical tunnel junctions consisting of alkanethiol molecules self-assembled on Au-coated Si substrates and contacted with Au-coated atomic force microscopy tips were characterized under varying junction loads in a conducting-probe atomic force microscopy configuration. Junction load was cycled in the fashion of a standard nanoindentation experiment; however, junction conductance rather than probe depth was measured directly. The junction conductance data have been analyzed with typical contact mechanics (Derjaguin-Müller-Toporov) and tunneling equations to extract the monolayer modulus (∼50 GPa), the contact transmission (-2 × 10-6), contact area, and probe depth as a function of load. The monolayers are shown to undergo significant plastic deformation under compression, yielding indentations ∼7 Å deep for maximum junction loads of ∼50 nN. Comparison of mechanical properties for different chain lengths was also performed. The film modulus decreased with the number of carbons in the molecular chain for shorter-chain films. This trend, abruptly reversed once 12 carbons were present along the backbone.