Al–Mg–Si alloys are heat-treatable and rely on precipitation hardening for their mechanical strength. We have employed the technique of muon spin relaxation to further our understanding of the complex precipitation sequence in this system. The muon trapping kinetics in a material reveals a presence of atom-sized defects, such as solute atoms (Mg and Si) and vacancies. By comparing the muon kinetics in pure Al, Al–Mg, Al–Si and Al–Mg–Si when held at different temperatures, we establish an interpretation of muon trapping peaks based on different types of defects. Al–Mg–Si samples have a unique muon trapping peak at temperatures around 200 K. This peak is highest for samples that have been annealed at 70–150 °C, which have microstructures dominated by a high density of clusters/Guinier–Preston zones. The muon trapping is explained by the presence in vacancies inside these structures. The vacancies disappear from the material when the clusters transform into more developed precipitates during aging.