Ionic liquid (IL)-protein interaction studies are well documented; nonetheless, some families of ILs possess high toxicity which leads to the perturbation of biomolecules. However, ILs can be suitably designed by tweaking the constituent ions and also by amalgamating the mixture that stabilises the protein against the denaturing effect of another IL. To address this, the present study has explored the role of IL mixtures in imparting structural stability to protein β-lactoglobulin (β-LG). Previously, it was demonstrated that choline iodide ([Chn][I]) had an adverse effect on the native structure of β-LG. In order to counteract the deleterious action of [Chn][I], four IL mixtures (choline acetate [Chn][Ac] + [Chn][I] (MCACI); choline bitartrate [Chn][Bit] + [Chn][I] (MCBCI); choline chloride [Chn][Cl] + [Chn][I] (MCCCI); and choline dihydrogenphosphate [Chn][Dhp] + [Chn][I] (MCDCI)) were prepared in different ratios and their effects on the structural stability of β-LG were investigated. The UV-visible and fluorescence spectroscopy results revealed that β-LG achieved conformational changes with the addition of aqueous solutions containing mixtures of these ILs as compared to [Chn][I] alone. In near UV-CD spectroscopy, we observed that these four mixtures of ILs preserved the structure of β-LG by maintaining the tertiary structure. The dynamic light scattering (DLS) results demonstrated that the aqueous solutions containing IL mixtures decreased the dH values of β-LG, eventually keeping the compact structure of β-LG. These results confirm that the four biocompatible IL mixtures reduce the unavoidable aggregates of β-LG in the presence of [Chn][I]. Additionally, from the thermal fluorescence analysis, it was observed that the thermal stability of β-LG was enhanced by the four IL mixtures, thus counteracting the deleterious effect of [Chn][I] on β-LG. To the best of our knowledge, this work for the first time has demonstrated the role of choline-based IL mixtures in the structural transition of β-LG. The IL mixtures successfully enhanced the stability of the protein by reducing the perturbation caused by one of the components of the IL mixtures, thus amplifying the advantages of the other components. Overall, these results might find implications for understanding the role of IL mixtures towards protein folding/unfolding and pave a new direction for the development of eco-friendly protein-protective additives.