Despite their ubiquity, self-assembled monolayers (SAMs) of thiols on coinage metals are difficult to study and are still not completely understood, particularly with respect to the nature of thiol–metal bonding. Recent advances in molecular electronics have highlighted this deficiency due to the sensitivity of tunneling charge-transport to the subtle differences in the overall composition of SAMs and the chemistry of their attachment to surfaces. These advances have also challenged assumptions about the spontaneous formation of covalent thiol–metal bonds. This paper describes a series of experiments that correlate changes in the physical properties of SAMs to photoelectron spectroscopy to unambiguously assign binding energies of noncovalent interactions to physisorbed disulfides. These disulfides can be converted to covalent metal–thiolate bonds by exposure to free thiols, leading to the remarkable observation of the total loss and recovery of length-dependent tunneling charge-transport. The identification and assignment of physisorbed disulfides solve a long-standing mystery and reveal new, dynamic properties in SAMs of thiols.