The adsorption and self-assembling properties of terephthalic acid (TPA) molecules deposited on Cu(001) at room temperature have been systematically studied with both experimental and theoretical tools. The system forms two phases at room temperature: the metastable β-phase and the stable (3 × 3) one. In the case of the β phase, low-energy electron diffraction and scanning tunneling microscopy (STM) results indicate that it has a (9√2 × 2√2) R45° unit cell with exactly the same molecular coverage as the (3 × 3) phase. In addition, the high-resolution X-ray photoelectron-spectroscopy spectra of the O 1s core level indicate that the irreversible β → (3 × 3) transition involves the following two processes: (i) deprotonation of the complete carboxyl groups remaining in the metastable phase and (ii) eventual rearrangement of the molecules into the 3 × 3 configuration. We explored possible molecular configurations for the β phase with different degree of deprotonation (including structures with Cu adatoms) by means of density functional theory calculations. Our theoretical results indicate the formation of strong bonds between the O atoms in carboxylates and the Cu atoms of the surface, which causes a bending of the molecules and a buckling of the first Cu layer. In the (3 × 3) phases, we show that the bending produces observable effects in the molecular STM images. Moreover, the strong interaction between the carboxylates and the Cu atoms at the step edges drives the reorientation of the surface steps along the ⟨100⟩ crystallographic directions.