Here we report on the effect of local molecular organization or “tertiary structure” on the charge transport properties of thiol-tethered tetraphenylporphyrin (ZnTPPF4-SC5SH) nanoscale clusters of ca. 5 nm in lateral dimension embedded within a dodecanethiol (C12) monolayer on Au(111). The structure of the clusters in the mixed monolayers and their resulting transport properties were monitored by Atomic Force Microscopy (AFM), Scanning Tunneling Microscopy (STM) and Spectroscopy (STS). The mixed films were deposited on Au(111) for a period of one to five days, during which the lateral dimensions of the ZnTPPF4-SC5SH islands that were formed after one day reduced by nearly 35% on average by five days, accompanied by a noticeable depletion of the surrounding C12 monolayer. These subtle changes in mixed monolayer morphology were accompanied by drastic differences in conductance. The ZnTPPF4-SC5SH clusters assembled for one day exhibited highly reproducible I–V spectra with simple tunneling behavior. By three days, this evolved into bias-induced switching of conductance, with a ∼100–1000 fold increase. Furthermore, current fluctuations started to become significant, and then dominated transport across the ZnTPPF4-SC5SH clusters assembled over five days. Our data suggests that this evolution can be understood by slow surface diffusion, enabling the ZnTPPF4-SC5SH molecules to overcome initial steric hindrance in the early stages of island formation in the C12 monolayer (at day one), to reach a more energetically-favored, close-packed organization, as noted by the decrease in island size (by day three). However, when desorption of the supporting matrix of C12 became pronounced (by day five), the ZnTPPF4-SC5SH clusters began to lose stabilization, and stochastic switching was then observed to dominate transport in the clusters, illustrating the critical nature of the local organization on these transport properties.