This work provides a detailed atom probe tomography study of clustering in the Al–Mg–Si system. Focus is on separating and understanding the influence of natural aging, preaging, and alloy composition on the clustering behavior of solute atoms. Two dilute alloys with the same total solute content have been studied, one Mg-rich and one Si-rich. The detrimental effect of natural aging for these alloys is investigated by comparing directly preaged samples to samples stored at room temperature before the preaging treatment. Clusters were identified in the atom probe datasets by the maximum separation method employing heuristically determined input parameters. It was found that seven days of intermediate natural aging gave a five times lower number density of clusters as compared to direct preaging for both alloy types. The clusters were of comparable size but their compositions depended on heat treatment history. Preaging promoted the formation of clusters with an Mg:Si ratio close to 1 in both alloys, while natural aging produced clusters with Mg:Si ratios more similar to those of the alloys.