The electroreduction of CO₂ (CO₂RR) is a promising strategy towards sustainable fuels. Cu is the only earth-abundant catalyst capable of CO₂-to-hydrocarbons conversion; yet, its dynamic structure under operando CO₂RR conditions remains unknown. Here, we track the Cu structure operando by electrochemical scanning tunneling microscopy and Raman spectroscopy. Surprisingly, polycrystalline Cu surfaces reconstruct forming Cu nanocuboids whose size can be controlled by the polarization potential and the time employed in their in-situ synthesis, without the assistance of organic surfactants and-or halide anions. If the Cu-surface is covered by a graphene monolayer, smaller features with enhanced catalytic activity for CO₂RR can be prepared. The graphene protecting layer soften the 3D morphological changes that Cu-based catalysts suffer when exposed to aggressive electrochemical environments, and allows us to track the kinetic roughening process. This novel strategy is promising for improving Cu long-term stability and, consequently, controlling product selectivity.