The biological relevance of amino acids is well known. They can be used as zwitterionic, cationic or anionic forms according to the pH of the medium where they are. Thus, our aim herein was to study the conformational preference of the polar amino acid l-threonine [C4H9NO3, (2S,3R)-2-amino-3-hydroxybutyric acid] under different pH conditions. A conformational study in an aqueous solution of the dissociation equilibrium of the amino acid l-threonine was carried out for this purpose. We recorded, at room temperature, the Mid-IR, Far-IR, Raman and VCD spectra of l-threonine from the aqueous solutions at pH values 5.70 (zwitterionic species), 1.00 (protonated species) and 13.00 (deprotonated species). The number of conformers found with the conformational search was 9 zwitterions, 27 anions and 52 cations. Both the study of the conformational landscape and the theoretical analysis of the vibrational features were accomplished by using DFT and ab initio calculations, that is, B3LYP/6-311++G(d,p) level of theory for all the conformers obtained from the conformational search, M062X/6-311++G(d,p) and MP2/6-311++G(d,p) levels of theory for the most stable conformers. The presence of water was included with the IEF-PCM implicit hydration model. With regard to the zwitterion, the importance of the analysis of the low frequency region (700–30 cm–1) in the Far-IR spectra should be noted, because it provides relevant information that can be used to determine the presence of the most stable structures.