This paper presents the modifications of the magnetic properties of Tb–Fe/Gd–Fe/Tb–Fe trilayer, displaying perpendicular magnetic anisotropy in the pristine state. Irradiation with Ar+ ions at a constant fluence of 1014 ions/cm2 with variable incident energies, in the range of 50–150 keV, corresponding to different penetration depths inside the trilayer films, was employed to obtain the tunability in magnetic properties of the trilayer assembly. A spin reorientation transition from perpendicular to the plane of the film could be ascertained even for the lowest energy of irradiation without any major structural modification. The isolated island-like larger magnetic domains, observed for the pristine films, no longer appeared after irradiation. The modifications of magnetic domains and hysteresis loops were understood using micromagnetic simulations, considering the depth-resolved variation of magnetic anisotropies of the top and middle layers. Our work shows a facile route to process anisotropy-engineered magnetic heterostructures using depth-sensitive external perturbation. © 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature.