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The use of dipolar aprotic solvents to swell lithiated Nafion ionomer membranes simultaneously serving as electrolyte and separator is of great interest for lithium battery applications. This work attempts to gain an insight into the physicochemical nature of a Li-Nafion ionomer material whose phase-separated nanostructure has been enhanced with a binary plasticiser comprising non-volatile high-boiling ethylene carbonate (EC) and sulfolane (SL). Gravimetric studies evaluating the influence both of mixing temperature (25 to 80 °C) and plasticiser composition (EC/SL ratio) on the solvent uptake of Li-Nafion revealed a hysteresis between heating and cooling modes. Differential scanning calorimetry (DSC) and wide-angle X-ray diffraction (WAXD) revealed that the saturation of a Nafion membrane with such a plasticiser led to a re-organisation of its amorphous structure, with crystalline regions remaining practically unchanged. Regardless of mixing temperature, the preservation of crystallites upon swelling is critical due to ionomer crosslinking provided by crystalline regions, which ensures membrane integrity even at very high solvent uptake (≈200% at a mixing temperature of 80 °C). The physicochemical properties of a swollen membrane have much in common with those of a chemically crosslinked polymer gel. The conductivity of ≈10−4 S cm−1 demonstrated by Li-Nafion membranes saturated with EC/SL at room temperature is promising for various practical applications.