The processes taking place during natural ageing (NA) of the aluminium alloy Al–0.4Mg–0.4Si (wt.%) are characterised by positron annihilation lifetime spectroscopy carried out both in situ during ageing and ex situ after cooling down samples to low temperatures (−180 °C to −60 °C) between NA steps. We find a pronounced dependence of positron lifetime on temperature, which is the signature of the presence of vacancy-free solute clusters in addition to vacancy-related defects. Such clusters are also found in as-quenched samples, indicating that clustering takes place already during quenching. The decomposition of positron lifetime spectra into various components allows us to apply the three-state trapping model and to determine the trapping rates into vacancy-related defects and solute clusters. By modelling the time dependence of positron data we are able to describe the natural ageing process as a gradual decrease of vacancy density associated with a pronounced increase of the density of solute clusters.