Variable-temperature scanning tunneling microscopy (STM) and spectroscopy (STS) measurements are performed on heptathioether β-cyclodextrin (β-CD) self-assembled monolayers (SAMs) on Au. The β-CD molecules exhibit very rich dynamical behavior, which is not apparent in ensemble-averaged studies. The dynamics are reflected in the tunneling current–time traces, which are recorded with the STM feedback loop disabled. The dynamics are temperature independent, but increase with increasing tunneling current and sample bias, thus indicating that the conformational changes of the β-CD molecules are induced by electrons that tunnel inelastically. Even for sample biases as low as 10 mV, well-defined levels are observed in the tunneling current–time traces. These jumps are attributed to the excitations of the molecular vibration of the macrocyclic β-CD molecule. The results are of great importance for a proper understanding of transport measurements in SAMs.