Abstract: In situ TEM is a valuable technique to offer novel insights in the behavior of nanomaterials under various conditions. However, interpretation of in situ experiments is not straightforward since the electron beam can impact the outcome of such measurements. For example, ligands surrounding metal nanoparticles transform into a protective carbon layer upon electron beam irradiation and may impact the apparent thermal stability during in situ heating experiments. In this work, we explore the effect of different treatments typically proposed to remove such ligands. We found that plasma treatment prior to heating experiments for Au nanorods and nanostars increased the apparent thermal stability of the nanoparticles, while an activated carbon treatment resulted in a decrease of the observed thermal stability. Treatment with HCl barely changed the experimental outcome. These results demonstrate the importance of carefully selecting pre-treatments procedures during in situ heating experiments.