The effects of residual NaNO3 on the modification of Cu/ZnO-Al2O3 catalysts have been extensively documented, but the modification mechanism is so far unclear. This work studies in detail the influence of the residual sodium nitrate present in the hydroxycarbonate precursors on their decomposition during calcination and how it affects to the formation and configuration of the final active sites of the Cu/ZnO-Al2O3 catalysts. Different samples with varying sodium content after washing (from 0.01 to 7.3 wt%) were prepared and studied in detail after calcination and reduction steps. The results of this work demonstrated that NaNO3 affects the decomposition mechanism of the hydroxycarbonate precursors during calcination and produces its decarbonation at low temperature. The enhancement of the decarbonation by NaNO3 leads to segregation and crystallization of CuO and ZnO with loss of mesostructure and surface area in the calcined catalysts. The loss of mesostructure in calcined catalysts affects the subsequent reduction step, decreasing the reducibility and damaging the nanostructure of the reduced catalysts forming large Cu particles in poor contact with ZnOx that results in a significant decrease in the intrinsic activity of the copper active sites for methanol synthesis.