Environmental transmission electron microscopy (ETEM) can provide unique insights into nanocarbon oxidation processes through atomic resolution and real time imaging of materials at high temperatures in reactive atmospheres. However, the electron beam can also influence the reaction rates, and even alter the processes entirely, complicating the interpretation of the in situ observations. Many mechanisms have been proposed to account for the impact of the electron beam, predominantly involving ionization of the oxidative gases to form more reactive species. However, these mechanisms have not been critically evaluated and compared to predictions from theory. Here, we evaluate the impact of the electron beam both qualitatively (oxidation mode and spatial extent) and quantitatively (oxidation rates), using high resolution imaging and electron energy loss spectroscopy, at different electron energies and dose rates. We demonstrate that transient defects generated by elastic scattering, forming highly active sites for carbon abstraction by oxygen, is the main mechanism for the enhanced oxidation rates observed in situ. This is evident from an insensitivity to electron energy and saturation of the effects at high electron dose rates. To avoid undue influence of the electron beam in future ETEM studies, we therefore recommend conditions where the intrinsic oxidation dominates over the beam-enhanced oxidation (note that no conditions are completely “safe”) and extensive comparisons with other methods. © 2023 The Author(s)