A combined DFT/vibrational spectroscopy approach is used to determine the interactions of the 1,3-dimethylimidazolium ([Mmim]+) and 1-ethyl-3-methylimidazolium ([Emim]+) cations and [BF4]− anions with each other in the liquid state and with Pd nanoparticles (NPs) immersed in ionic liquids (ILs) composed of these ions. Formation of aggregates of the counter-ions in the liquid does not have a strong influence on the interaction energy of the IL components with the palladium clusters used to model NPs, which is smaller than the energy of addition of a Pd atom to the cluster. Stronger Pd–Pd interactions in comparison to the interactions of the palladium cluster with the IL suggest kinetic stabilisation of Pd-NPs in 1,3-dialkylimidazolium tetrafluoroborates rather than thermodynamic stabilisation. Moreover, the palladium clusters interact more strongly with the anions than with the cations, and this suggests an important role of the anions in formation and stabilisation of Pd-NP in ILs. At the same time, binding between an isolated Pd atom and [Mmim]+ cation is stronger than Pd–[BF4]− binding. IR and Raman spectral simulations reveal that surface-enhanced Raman spectroscopy is much less sensitive to interactions of Pd-NPs with the [BF4]− anion compared to interactions with [Mmim]+ cations. In contrast, IR spectroscopy is better suited to study the anion–metal interactions, whereas IR spectral manifestations of the cation–metal interactions are rather modest. The splitting of the strong νas(BF4−) IR band into three components appears to be a convenient spectroscopic marker for Pd–[BF4]− interactions, which is confirmed by actual spectra of Pd-NPs stabilised by [Emim][BF4]. The IR spectra and their assignment with quantum chemical computations suggest that both the anions and cations of [Emim][BF4] interact with the Pd-NP surface in the IL. The cation ring orientation close to the surface normal appears to be the dominant interaction. The anion is bound to the surface through either two or three fluorine atoms.