We observed the dynamic behaviour of a single conjugated molecule, 4-biphenylmethanethiol (BPMT), inserted in a self-assembled monolayer (SAM) matrix of a bicyclo[2.2.2]octane derivative (BCO) using scanning tunnelling microscopy at ∼110 K. At room temperature (Wakamatsu et al 2003 Nanotechnology 14 258), stochastic switching of BPNT and lateral movement of the BPMT and the BCO molecules were observed even in the well-ordered BCO SAM matrix on Au(111) terraces. Such movement was, however, rarely observed in the SAM on Au(111) terraces at ∼110 K. Single BPMT molecules were fixed in the well-ordered BCO SAM matrix at ∼110 K, except at step edges and edges of one atom deep pits of the Au(111) substrate. When a disordered BCO SAM matrix was created intentionally by applying voltage pulses, the stochastic switching of the single BPMT molecule and the lateral movement of the BCO and the BPMT molecules were observed more frequently than those at the step edges and the pit edges at ∼110 K.