Ionic liquids generally display peculiar structural features that impact their physical properties, such as the formation of polar and apolar domains. Recently, ionic liquids functionalized with anthraquinone and TEMPO redox groups were shown to increase the energy storage performance of supercapacitors, but their structure has not yet been characterized. In this work, we use polarizable molecular dynamics to study the nanostructuration of such biredox ionic liquids. We show that TEMPO nitroxyl functions tend to aggregate, while the anthraquinone groups favor stacked arrangements. The latter eventually percolate through the whole liquid, which sheds some light on the mechanisms at play within biredox ionic liquid-based supercapacitors.