The precipitate microstructure and vacancy distribution in Al-Mg-Si alloys with different amounts of solute and different heat treatments were investigated by transmission electron microscopy and muon spin relaxation measurements. A high amount of vacancies is normally present in Al-Mg-Si alloys as these bind to atomic clusters. We observe these vacancies to leave the material not before over-aging at very high temperatures such as 623 K (350 °C), meaning that vacancies do not bind to incoherent over-aged precipitates. For samples only stored at room temperature after solution heat treatment, a reduction of muon trapping was found at a temperature of 140 K (−133 °C) when reducing the amount of solute in the alloy. This might be connected to a lower number density of Cluster (1), which contrary to Cluster (2) do not nucleate precipitates upon further aging of the material.