Self-assembled quantum dots (QDs) have attracted significant attention because of their potential applications in novel semiconductor devices. In this work, we investigated radiation effects induced by 1.0 MeV proton ion beams on InAs self-assembled quantum dots. In particular, we emphasized the effects of lattice environments of QDs on their luminescence emission after ion beam irradiation. Photoluminescence (PL) spectroscopy was used to characterize the optical properties of QDs subjected to proton irradiation and post-irradiation annealing. Compared to the single-layer QDs grown in GaAs films, the QDs embedded in an AlAs/GaAs superlattice exhibited much higher PL degradation resistance to proton beam bombardment, e.g., at the highest dose (1.0×1014 cm−2) used in this work, a difference of ~ 20-fold in PL intensity was found between the QDs configured in these two different lattice structures. After thermal annealing of irradiated QD samples, ion beam enhanced blueshift of PL was observed to be much more pronounced for the single-layer QDs. We discuss mechanisms that may result in the differences in optical response to ion beams between QDs with different lattice surroundings.