Two different precipitate hardening aluminium alloys processed by friction stir welding were investigated. The microstructure and the hardness of the as delivered materials were compared to that of the weld nugget. Transmission electron microscopy observations combined with three-dimensional atom probe analyses clearly show that beta; precipitates dissolved in the nugget of the Al-Mg-Si giving rise to some supersaturated solid solution. It is shown that the dramatic softening of the weld could be partly recovered by post-welding ageing treatments. In the Al-Mg-Sc alloy, Al3Sc precipitate size and density are unchanged in the nugget comparing to the base metal. These precipitates strongly reduce the boundary mobility of recrystallised grains, leading to a grain size in the nugget much smaller than in the Al-Mg-Si alloy. Both coherent and incoherent precipitates were detected. This feature may indicate that a combination of continuous and discontinuous recrystallisation occurred in the weld nugget.