Transition metal phosphorous trisulfides (TMPTs) are inorganic materials with inherent magnetic properties. Due to their layered structure, they can be exfoliated into ultra-thin sheets, which show properties different from their bulk counterparts. Herein, we present a detailed analysis of the interaction of the electron beam (30−80 kV) in a transmission electron microscope with freestanding few-layer TMPTs, with the aim of tailoring their properties. The irradiation-induced structure modifications were systematically investigated by various transmission electron microscopy methods on FePS 3 , MnPS 3 , and NiPS 3 , and the results are rationalized with the help of ab initio calculations, which predict that the knock-on threshold for removing sulfur is significantly lower than that for phosphorus. Therefore, a targeted removal of sulfur is feasible. Eventually, our experiments confirm the dose-dependent, predominant removal of sulfur by the impinging electrons, thus showing the possibility of tuning the sulfur concentration. Using ab initio calculations, we analyze the electronic structure of the TMPTs with single vacancies and oxygen impurities and predict distinct electronic properties depending on the type of defect. Therefore, our study shows the possibility of tuning the properties of ultra-thin freestanding TMPTs by controlling their stoichiometry.