The microstructure and morphology of the surface of aluminium alloys strongly affect the nucleation, growth, and protective properties of chromate conversion coatings. Samples of AA 2024-T3 cladded with AA1230 were pretreated with two different procedures before they underwent a chromating process, which consisted of dipping in a commercial Alodine 1200 solution. In one procedure, an extra step, consisting of immersion in nitric-hydrofluoric acid solution for 30 s (desmutting bath), was carried out after immersion in sulfuric -phosphoric acid solution (acid pickling bath). Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM) and electrochemical investigations highlighted the fact that this extra step in the pretreatment route gave rise to a more etched, but less reactive surface, due to the removal of a large amount of cathodic sites, mainly related to Al-Fe-Si precipitates present in the clad layer. A similar effect, but on a smaller scale, was caused also by the increase of the time of immersion in sulfuric -phosphoric acid solution. The decrease of galvanic coupling gives rise to a more homogeneous nucleation of the chromate conversion coating on the surface of the Alclad 2024-T3. Moreover, the chromate film tends to be denser and with fewer defects.