This study reports the synthesis and comprehensive characterization of five fluorinated ionic liquids (FILs), each composed of an imidazolium cation of varied fluoroalkyl chain lengths paired with a fluorinated anion: a newly developed aromatic sulfonamide, bistriflimide (Tf 2 N), or iodide. The relationship between molecular structure and physical properties, including thermal behavior, density, and viscosity, is reported. The identity of the anion has the strongest effect on both thermal stability and thermal behavior, whereas elongation of the fluorinated alkyl chain of the cation more strongly influences density and viscosity. These observations suggest nanosegregation within the liquid and the formation of three microphases (polar, nonpolar, and fluorous). We then evaluate the solubilities of commonly used hydrofluorocarbon refrigerant gases, HFC-32 (difluoromethane) and HFC-125 (pentafluoroethane), in the neat and encapsulated FILs, comparing their performance against commercially available ionic liquids (ILs). We find higher solubilities of HFC-32 in the FILs relative to nonfluorinated commercial ILs that exhibited greater solubility of HFC-125, highlighting selective gas absorption. Additionally, we observe that encapsulated FILs exhibit trends in gas uptake analogous to those of neat FILs. This work not only contributes to a deeper understanding of the structure−property relationships in FILs but also presents promising avenues for their utilization in HFC gas uptake and separation processes, emphasizing the potential of encapsulated FILs as a viable technology to overcome challenges associated with high viscosities of ILs in bulk processing.