Ion beam depth profiling is increasingly used to investigate layers and interfaces in complex multilayered devices, including solar cells. This approach is particularly challenging on hybrid perovskite layers and perovskite solar cells because of the presence of organic/inorganic interfaces requiring the fine optimization of the sputtering beam conditions. The ion beam sputtering must ensure a viable sputtering rate on hard inorganic materials while limiting the chemical (fragmentation), compositional (preferential sputtering) or topographical (roughening and intermixing) modifications on soft organic layers. In this work, model (Cs_x(MA_0.17FA_0.83)_100−xPb(I_0.83Br_0.17)₃/cTiO₂/Glass) samples and full mesoscopic perovskite solar cells are profiled using low-energy (500 and 1000 eV) monatomic beams (Ar⁺ and Cs⁺) and variable-size argon clusters (Ar_n⁺, 75 < n < 4000) with energy up to 20 keV. The ion beam conditions are optimized by systematically comparing the sputtering rates and the surface modifications associated with each sputtering beam. X-ray photoelectron spectroscopy, time-of-flight secondary ion mass spectrometry, and in-situ scanning probe microscopy are combined to characterize the interfaces and evidence sputtering-related artifacts. Within monatomic beams, 500 eV Cs⁺ results in the most intense and stable ToF-SIMS molecular profiles, almost material-independent sputtering rates and sharp interfaces. Large argon clusters (n > 500) with insufficient energy (E < 10 keV) result in the preferential sputtering of organic molecules and are highly ineffective to sputter small metal clusters (Pb and Au), which tend to artificially accumulate during the depth profile. This is not the case for the optimized cluster ions having a few hundred argon atoms (300 < n < 500) and an energy-per-atom value of at least 20 eV. In these conditions, we obtain (i) the low fragmentation of organic molecules, (ii) convenient erosion rates on soft and hard layers (but still different), and (iii) constant molecular profiles in the perovskite layer, i.e., no accumulation of damages.