The effect of sample preparation on a pre-aged Al–Mg–Si–Cu alloy has been evaluated using atom probe tomography. Three methods of preparation were investigated: electropolishing (control), Ga+ focused ion beam (FIB) milling, and Xe+ plasma FIB (PFIB) milling. Ga+-based FIB preparation was shown to introduce significant amount of Ga contamination throughout the reconstructed sample (≈1.3 at%), while no Xe contamination was detected in the PFIB-prepared sample. Nevertheless, a significantly higher cluster density was observed in the Xe+ PFIB-prepared sample (≈25.0 × 1023 m−3) as compared to the traditionally produced electropolished sample (≈3.2 × 1023 m−3) and the Ga+ FIB sample (≈5.6 × 1023 m−3). Hence, the absence of the ion milling species does not necessarily mean an absence of specimen preparation defects. Specifically, the FIB and PFIB-prepared samples had more Si-rich clusters as compared to electropolished samples, which is indicative of vacancy stabilization via solute clustering.