Gallium ion (Ga+) beam damage induced indium (In) precipitation in indium gallium arsenide (InGaAs)/indium aluminium arsenide (InAlAs) multiple quantum wells and its corresponding evolution under electron beam irradiation was investigated by valence electron energy loss spectroscopy (VEELS) and high‐angle annular dark‐field imaging (HAADF) in scanning transmission electron microscopy (STEM). Compared with argon ion milling for sample preparation, the heavier projectiles of Ga+ ions pose a risk to trigger In formation in the form of tiny metallic In clusters. These are shown to be sensitive to electron irradiation and can increase in number and size under the electron beam, deteriorating the structure. Our finding reveals the potential risk of formation of In clusters during focused ion beam (FIB) preparation of InGaAs/InAlAs quantum well samples and their subsequent growth under STEM‐HAADF imaging, where initially invisible In clusters of a few atoms can move and swell during electron beam exposure.Lay description: In this paper, the evolution of Ga+ implantation induced In precipitation in InGaAs/InAlAs multiple quantum wells under electron beam irradiation was investigated by valence electron energy loss spectroscopy (VEELs), energy dispersive X‐ray spectroscopy (EDXs) and high‐angle annular dark‐field (HAADF) imaging technique based in a probe aberration corrected scanning transmission electron microscope. In contrast to Ar+ ion bombardment, the projectile of focused Ga+ ions is able to trigger the clustering of In interstitials in InGaAs/InAlAs multiple quantum wells, which allows the formation of metallic In precipitates. Afterwards, by exploiting an extensive electron beam rastering on the region of In precipitation, the increase of electron irradiation time could lead to a pronounced swelling of In cluster size. Especially for the region contains In precipitates of several atoms, where the morphology of In cluster is invisible in atomic image. The continuous electron irradiation could give rise to the promotion of In clustering, allowing the structure of In precipitates been resolved by HAADF image. Our finding reveals the potential risk of formation of In precipitates during focused Ga+ ion beam bombarded InGaAs/InAlAs semiconductors and the subsequent evolution of In clustering under electron beam rastering. These findings emphasise the need for caution when studying FIB prepared In‐based III–V quantum well specimens using TEM even in the In(Ga,Al)As system, as the initially formed In‐rich clusters are so small they can remain invisible for some time.