In situ electron irradiation effects on shape and size of plate-like Ag nanoparticles (NPs) embedded in silicon nitride self-standing approximate to 70-nm-thick membranes are investigated as a function of the beam energy (120, 160 and 200 keV) and fluence using a conventional transmission electron microscope. The irradiations are performed at room temperature and cause a rapid spheroidization of the initially observed plate-like structures. Preferential sputtering of N and Si atoms exposes the resulting Ag NPs to the vacuum. At this point the sputtering of the Ag atoms causes a size decrease at distinct rates depending on the NP size and on the beam energy. This is modeled considering the influence of a size-dependent surface binding of the Ag atoms on the sputtering process. The results are compared with literature models for size-dependent cohesive energy. Our experiments discloses a new way to modify sizes and shapes and test for the size-dependent properties of thermally unstable nanoscopic objects.