Terephthalic acid on metal surfaces is a system of high interest for interfacial layers as well as for use in generating surface nanostructures by supramolecular self-assembly. Here we demonstrate structural transitions upon compression of the first layer as well as a significant transition from a flat lying chemisorbed first monolayer to a standing second layer. The second layer structure is stable at 150 °C, but a weakly bound state is observed to desorb molecularly below that temperature, likely a transient mobile state during annealing. Molecular resolution scanning tunnelling microscopy is complemented by X-ray photoelectron spectroscopy and thermal desorption spectroscopy in this study. These results provide general insight in the development of self-assembled organic thin films at surfaces, especially with regard to the nature of the metal/organic interface and growth transitions to maximize first layer packing and obtain a second layer that bridges commensurability with the substrate and a more bulk-like structure.