Self-assembled tereplithalic acid adlayers on a Cu(100) surface have been studied by X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure, and scanning tunneling microscopy in the temperature range 190-400 K under ultrahigh vacuum conditions. We observe three distinct well-ordered phases evolving with increasing temperature. The combined data analysis reveals that thermally activated deprotonation of molecular carboxyl groups is decisive in the irreversible transformation of the respective structures. Their self-assembly is mediated by changing intermolecular hydrogen bond configurations, whereby a flat adsorption geometry is retained.