The damage generation and its annealing behavior in GaAs/(Ga,Al)As quantum wells after Ga+implantation at room temperature is investigated by transmission electron microscopy. Its relations with the disordering of the layered structures is explored by low temperature photoluminescence spectroscopy. We find that at low doses the intermixing is activated during annealing through the diffusion of point defects, while at high doses the disordering is produced by cascade mixing. A strong segregation of the defects in the GaAs layers is observed. During implantation of a GaAs/Ga0.65Al0.35As single quantum well, the GaAs quantum‐well layer accumulates damage more rapidly than the Ga0.65Al0.35As barriers. At high dose this leads to a differential amorphization of the two compounds. Using the critical damage energy density model, the amorphization thresholds of GaAs and Ga0.65Al0.35As are estimated around 26 eV/molecule and 960 eV/molecule, respectively, in our conditions of implantation. The influence of barriers in AlAs is studied. AlAs is more resistant to amorphization than Ga0.65Al0.35As and delays the amorphization of the GaAs quantum‐well layer. This effect is attributed to thein siturecombination of point defects during irradiation in AlAs material as well as to some intermixing of the layers. After annealing it appears that defects can easily diffuse in Al rich materials but are trapped in GaAs. It is concluded that the ability of AlAs to prevent damage accumulation in GaAs quantum wells and to drain off the defects during annealing can be exploited for device applications. The general trends for an optimized GaAs/GaAlAs quantum well dedicated to mixing applications such as the fabrication of quantum‐well wires by masked implantation is finally proposed.