The temperature dependence of the far- and mid-infrared spectrum of two prototypical protic ionic liquids (PILs) sharing a common trialkylammonium cation, but having different anions, is investigated. The exploitation of both the FIR and MIR ranges provides complementary information about the microscopic configurations and the intermolecular interactions, which determine the structure and the properties of ILs. The analysis of the data collected for all the measured frequencies in a wide temperature range reveals several phase transitions and allows the evaluation of the conformer distribution in the different physical states. The difference in the average energy between the H-bonded configurations and the dispersion-governed ones was also determined for the two PILs. Moreover, a computational model for ionic couples based on the ωB97X-D functional and a polar solvent is here successfully exploited for the description of the hydrogen bonding between anion and cation. For the attribution of vibrational lines of the conformers of the cation, the picture based on single ion calculations at the B3LYP level is more valuable and provides better agreement with the experiments.