Chemistry of the Au-S interface at the nanoscale is one of the most complex systems to study, as the nature and strength of the Au-S bond change under different experimental conditions. In this study, using mechanically controlled break junction technique, we probed the conductance and analyzed Flicker noise for several aliphatic and aromatic thiol derivatives and thioethers. We demonstrate that Flicker noise can be used to unambiguously differentiate between stronger chemisorption (Au-SR) and weaker physisorption (Au-SRR′) type interactions. The Flicker noise measurements indicate that the gold rearrangement in chemisorbed Au-SR junctions resembles that of the Au rearrangement in pure Au-Au metal contact breaking, which is independent of the molecular backbone structure and the resulting conductance. In contrast, thioethers showed the formation of a weaker physisorbed Au-SRR′ type bond, and the Flicker noise measurement indicates the changes in the Au-anchoring group interface but not the Au-Au rearrangement like that in the Au-SR case. Additionally, by employing single-molecular conductance and Flicker noise analysis, we have probed the interfacial electric field-catalyzed ring-opening reaction of cyclic thioether under mild environmental conditions, which otherwise requires harsh chemical conditions for cleavage of the C-S bond. All of our conductance measurements are complemented by NEGF transport calculations. This study illustrates that the single-molecule conductance, together with the Flicker noise measurements can be used to tune and monitor chemical reactions at the single-molecule level.