The recent development of liquid cell (scanning) transmission electron microscopy (LC-(S)TEM) has opened the unique possibility of studying the chemical behavior of nanomaterials down to the nanoscale in a liquid environment. Here, we show that the chemically induced etching of three different types of silica-based silica nanoparticles can be reliably studied at the single particle level using LC-(S)TEM with a negligible effect of the electron beam, and we demonstrate this method by successfully monitoring the formation of silica-based heterogeneous yolk-shell nanostructures. By scrutinizing the influence of electron beam irradiation, we show that the cumulative electron dose on the imaging area plays a crucial role in the observed damage and needs to be considered during experimental design. Monte-Carlo simulations of the electron trajectories during LC-(S)TEM experiments allowed us to relate the cumulative electron dose to the deposited energy on the particles, which was found to significantly alter the silica network under imaging conditions of nanoparticles. We used these optimized LC-(S)TEM imaging conditions to systematically characterize the wet etching of silica and metal(oxide)-silica core-shell nanoparticles with cores of gold and iron oxide, which are representative of many other core-silica-shell systems. The LC-(S)TEM method reliably reproduced the etching patterns of Stöber, water-in-oil reverse microemulsion (WORM), and amino acid-catalyzed silica particles that were reported before in the literature. Furthermore, we directly visualized the formation of yolk-shell structures from the wet etching of Au@Stöber silica and Fe