Here, we investigated the influence of the nanoscale surface morphology on the electrostatic double layer at corrugated surfaces in aqueous electrolytes. For this purpose, we have produced cluster-assembled nanostructured zirconium dioxide (ns-ZrO x, x ≈ 2) films with controlled morphological properties by supersonic cluster beam deposition (SCBD) and measured the double-layer interaction by atomic force microscopy with colloidal probes. SCBD allowed tuning the characteristic widths of the corrugated interface (root-mean-square roughness, correlation length) across a wide range of values, matching the width of the electrostatic double layer (Debye length) and the typical size of nanocolloids (proteins, enzymes, and catalytic nanoparticles). To accurately characterize the surface charge density in the high-roughness regime, we have developed a two-exponential model of the electrostatic force that explicitly includes roughness and better accounts for the roughness-induced amplification of the interaction. We were then able to observe a marked reduction of the isoelectric point of ns-ZrO x surfaces of increasing roughness. This result is in good agreement with our previous observations on cluster-assembled nanostructured titania films and demonstrates that the phenomenon is not limited to a specific material, but more generally depends on peculiar nanoscale morphological effects, related to the competition of the characteristic lengths of the system.