In this work, we investigate the effect of the cation structure on the structure and dynamics of the electrode–electrolyte interface using molecular dynamics simulations. A constant potential method is used to capture the behaviour of 1-ethyl-3-methylimidazolium bis (trifluoromethane)sulfonimide ([C2mim][NTf2]) and butyltrimethylammonium bis(trifluoromethane) sulfonimide ([N4,1,1,1][NTf2]) ionic liquids at varying potential differences applied across the supercapacitor. We find that the details of the structure in the electric double layer and the dynamics differ significantly, yet the charge profile and capacitance do not vary greatly. For the systems considered, charging results in the rearrangement and reorientation of ions within ∼1 nm of the electrode rather than the diffusion of ions to/from the bulk region. This occurs on timescales of O(10 ns) for the ionic liquids considered, and depends on the viscosity of the fluid.