The stability and non‐covalent interactions (NCI) of complexes formed by pinocembrin (PC), pinobanksin (PB), and pinobanksin 3‐acetate (PA) with a series of imidazolium‐based ionic liquids ([Bmim][BF4], [Bmim][Br], [Omim][Br], [Umim][Br], [OmimOH][Cl], and [UnmimOH][Br]) were evaluated through thermochemical parameters obtained from density functional theory (DFT) calculations, as well as atoms in molecules (AIM) and NCI analyses. The theoretical data were contrasted with experimental results obtained from the extraction of the three phenolic compounds from a propolis sample with aqueous solutions of the imidazolium salts. Calculations predicted that the complex formation processes at 298 K are spontaneous and close to the thermodynamic equilibrium (ΔGm ± 10 kcal/mol) in all the cases. However, [Omim][Br] forms the more stable complexes with the three flavonoids, which present a good correlation with greater amounts of PC, PB, and PA obtained during the extractions with this salt, with respect to the others. The hydrogen bond between the anion and the hydroxyl group of phenolic type is one of the most important NCI between the chemical species that conform the complexes; however, the functionalized cation UnmimOH+ can interact, even better than bromide, with the flavonoids through a hydrogen bond between hydroxyl groups. This could explain the higher values obtained through the Folin–Ciocalteu test used to evaluate the total phenolic content in the propolis extracts. This is not the case for the OmimOH+ functionalized cation, because the more electronegative counterion (Cl−) avoids an analogous behavior.