Ionic Liquids (ILs) are a specific class of molecular electrolytes characterized by the total absence of co-solvent. Due to their remarkable chemical and electrochemical stability, they are prime candidates for the development of safe and sustainable energy storage systems. The competition between electrostatic and van der Waals interactions leads to a property original for pure liquids: they self-organize in fluctuating nanometric aggregates. So far, this transient structuration has escaped to direct clear-cut experimental assessment. Here, we focus on a imidazolium based IL and use particle-probe rheology to (i) catch this phenomenon and (ii) highlight an unexpected consequence: the self-diffusion coefficient of the cation shows a one order of magnitude difference depending whether it is inferred at the nanometric or at the microscopic scale. As this quantity partly drives the ionic conductivity, such a peculiar property represents a strong limiting factor to the performances of ILs-based batteries.