Technological advancement towards the quantum era requires secure communication, quantum computation and ultra-sensitive sensing capabilities. Layered quantum materials (LQMs) have remarkable optoelectronic and quantum properties that can usher us into the quantum era. Electron microscopy is the tool of choice for measuring these LQMs at an atomic and nanometre scale. On the other hand, electron-irradiation of LQMs can modify various material properties, including the creation of structural defects. We review different types of structural defects, as well as electron elastic-and inelastic-scattering induced processes. Controlled modification of optoelectronic and quantum properties of LQMs using electron-irradiation, including creation of single-photon emitters is discussed. Protection of electron-irradiation induced damage of LQMs via encapsulation by other layered materials is encouraged. We finally give insights into challenges and opportunities, including creating novel structures using an electron beam.