Molecular self-assembly at surfaces proceeds through complex selective pathways involving not only the recognition of molecular structures based on lock-and-key interactions, but also the existence of effective methods of dynamical search and trial. This becomes especially crucial when a mixture of different molecules with immiscible shapes results in the segregation of mesoscopic separated phases. For example, this is the case in the formation of large homochiral phases from a racemic mixture of chiral molecules at surfaces. Large-scale mass transport through thermally activated diffusion has been proposed as the mechanism leading to phase segregation. However, it is not clear how molecules of one species can move for large distances, in many cases overcoming barriers associated with topological defects such as monoatomic steps. In solution, the conformational dynamics of molecules with internal flexibility plays an important role in supramolecular assembly. For example, the folding structure of proteins or peptides is governed by dynamical stochastic mapping of multidimensional conformational configurations. A metal surface represents in turn a rigid object interacting with the molecular adsorbates, in many cases very strongly compared to the magnitude of thermal energy at room temperature. In spite of that, thermally activated conformational changes have been identified at the single-molecule scale, which implies that internal degrees of freedom may also be active during the recognition and growth of molecular thin films at surfaces. Whether they play a crucial role in the mesoscopic ordering and phase separation is not yet clear. Here, we use low-temperature (5 K) scanning tunneling microscopy (STM) to statistically track the different molecular structures of an azobenzene derivative adsorbed on a gold surface. We find that the ratio between different azobenzene rotamers changes in response to an increase in temperature and coverage, thus proving that intramolecular conformational dynamics is an active pathway of molecular recognition during the formation of large-scale molecular assemblies on surfaces. Our study is performed on 3,3’-di(methoxycarbonyl)azobenzene (CMA) deposited on a Au ACHTUNGTRENNUNG(111) surface. A gold substrate is employed because it leads to weak molecular adsorption, thus maximizing the role of intermolecular interactions. CMA is formed by an azobenzene skeleton functionalized with a carboxymethyl end group at one of the meta sites of the phenyl rings (see Figures 1a and b). The methyl part of the end group