The analysis of nanomaterials by electron microscopy-based techniques has brought huge progress in the general comprehension of the matter at the sub-nanometric scale. Some materials remain however difficult to investigate, in particular by transmission electron microscopy due to their instability under a highly energetic electron beam. Zeolites, which play a key role in nowadays societies, belong to this category of beam sensitive materials. Therefore, their instability under the beam has sparked the interest in understanding the source of the damage and furtherly providing clues to circumvent it. In this review a brief excursus on the common mechanisms of material degradation under electron exposure is proposed, considering the type of interaction between the highly energetic electrons and the specimen. The phenomenology of the damage in zeolites is also described, evoking the observable effects, such as the amorphization and anisotropic shrinkage of zeolitic grains but also the eventual bubble formation and metallic precipitation of the stabilizing cationic agents. Ionization mechanisms are then imputable for explaining the observed phenomena, from the radiolytic process responsible for generating strain centers to charging effects which can lead to ionic currents inside the specimen. However, the research on the application of electron microscopy for zeolite study has progressed with the purpose of reducing the damaging effects. From the optimization of the preparation protocol to the introduction of highly advanced TEM techniques, nowadays it is possible to reach a sub-Angstrom resolution and probe single framework and non-framework atoms, before irreversibly compromising the zeolite's structure and morphology.