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Abstract While many mechanistic studies have focused on the lubricious properties of ionic liquids (ILs) on ideally smooth surfaces, little is known about the mechanisms by which ILs lubricate contacts with nanoscale roughness. Here, substrates with controlled density of nanoparticles are prepared to examine the influence of nanoscale roughness on the lubrication by 1‐hexyl‐3‐methyl imidazolium bis(trifluoromethylsulfonyl)imide. Atomic force microscopy is employed to investigate adhesion, hydrodynamic slip, and friction at the lubricated contact as a function of surface topography for the first time. This study reveals that nanoscale roughness has a significant influence on the slip along the surface and leads to a maximum slip length on the substrates with intermediate nanoparticle density. This coincides with the minimum friction coefficient at sufficiently small contact stresses, likely due to the lower resistance of the IL film to shear. However, at the higher pressures applied with a sharp tip, friction increases with nanoparticle density, indicating that the IL is not able to alleviate the increased dissipation due to roughness. The results of this work point toward a complex influence of the surface topology on friction. This study can help design ILs and nanopatterned substrates for tribological applications and nano‐ and microfluidics.