Liquid phase transmission electron microscopy (LP‐TEM) is a novel and highly promising technique for the in situ study of important nanoscale processes, in particular the synthesis and modification of various nanostructures in a liquid. Destabilization of the samples, including reduction, oxidation, or dissolution by interactions between electron beam, liquid, and sample, is still one of the main challenges of this technique. This work focuses on amorphous silica nanospheres and the phenomena behind their reshaping and dissolution in LP‐TEM. It is proposed that silica degradation is primarily the result of reducing radical formation in the liquid phase and the subsequent accelerated hydroxylation of the silica, while alterations in silica solid structure, pH, and oxidizing species formation had limited influence. Furthermore, the presence of water vapor instead of liquid water also results in degradation of silica. Most importantly however, it is shown that the addition of scavengers for reducing radicals significantly improved amorphous silica stability during LP‐TEM imaging. Devising such methods to overcome adverse effects in LP‐TEM is of the utmost importance for further development and implementation of this technique in studies of nanoscale processes in liquid.