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Abstract This research is a significant step forward in understanding how the electrochemical cell setup influences CO2 conversion. The performance of Cu–Zn–Al metal oxide-based catalysts was compared in two reactor configurations: a gas diffusion electrode (GDE) cell with an aqueous electrolyte and a Membrane Electrode Assembly (MEA) cell operating in the gas phase without catholyte. The different operations induced significant morphological and crystalline structural changes, profoundly impacting the catalytic behaviour. The MEA configuration, for instance, led to the formation of a higher Cu0/Cu1+ ratio in the catalysts, promoting C–C coupling for C2H4 production. Conversely, the GDE operation favoured alcohol (ethanol and methanol) production by balancing copper oxidation states formed in situ in the presence of the aqueous catholyte. Zn and Al oxides also played a role in stabilising the resulting Cu species, some of which remained oxidised on the electrode surface. These findings underscore the crucial influence of varying cell operation conditions on catalyst reconstruction, shaping the quantity of Cu0 + Cu1+ species formed in situ to tailor catalyst selectivity.