The intra- and intermolecular interactions in ether-functionalized ionic liquids (ILs) are studied by means of infrared (IR) spectroscopy measurements of N-ethoxyethyl-N-methylpiperidiniumbis(fluorosulfonyl)imide (P1,2O2-FSI) and N-ethoxyethyl-N-methylmorpholiniumbis(fluorosulfonyl)imide (M1,2O2-FSI). The temperature dependence of the spectra in the medium IR range allows the study of the anion conformer distribution and its variation during phase transitions. In particular, it is found that for both ILs the trans conformer of FSI is more stable than the cis conformer, and the enthalpy differences between them are calculated and are found to decrease upon the addition of a Li salt. The results obtained in the far IR range, combined with ab initio calculation of the ionic couple performed using the B3LYP-D functional and considering both empirical dispersion corrections and the presence of a polar solvent, provide evidence for the occurrence of a hydrogen bonding between the O atom of the anion and its closest H atoms directly linked to a C atom of the cation. The comparison with samples having the same cations but with bis(trifluoromethanesulfonyl)imide (TFSI) as an anion, that is, M1,2O2-TFSI and P1,2O2-TFSI, as well as with samples having cations without the ether-functionalization neither in the ring nor in the side chain, such as N-propyl-N-methylpyrrolidinium-FSI (PYR13-FSI) and 1-butyl-1-methylpyrrolidinium-TFSI (PYR14-TFSI), indicates that the occurrence of such highly directional interaction between anion and cation is better observable in the ether-functionalized samples, in particular in those containing FSI as an anion.