Imidazolium Ionic Liquids (ILs) have been found to exhibit unusual nanostructuring behavior below their glass transition temperatures (Tg), which is ascribed to rearrangements in nonpolar domains formed by segregated alkyl chains. However, the dimensions required for such highly cooperative bulk phenomena are still unknown. In this work, we for the first time, investigate the effect of nanoconfinement on structural anomalies in imidazolium ILs. For this purpose, a series of ILs were embedded into the cavities of metal-organic framework (MOF) ZIF-8 and investigated using spin probes and Electron Paramagnetic Resonance (EPR) spectroscopy. The unusual nanostructuring near Tg, previously known for bulk ILs, was also observed for such nanoconfined ILs, and the amplitude of the anomaly was found to be dependent on the structure of the IL, thus showing the effects of molecular packing inside the MOF cavity. The first observation of structural anomalies in nanoconfined ILs opens perspectives for designing smart materials exhibiting these phenomena, and engaging MOFs as platforms creates the basis for potential applications of such functionalities.