An in situ electron energy loss spectroscopy (EELS) technique has been developed to investigate the dynamic processes associated with electron-beam nanofabrication on thin membranes. In this article, practical applications germane to e-beam nanofabrication are illustrated with a case study of the drilling of nanometer-sized pores in silicon nitride membranes. This technique involves successive acquisitions of the plasmon-loss and the core-level ionization-loss spectra in real time, both of which provide the information regarding the hole-drilling kinetics, including two respective rates for total mass loss, individual nitrogen and silicon element depletion, and the change of the atomic bonding environment. In addition, the in situ EELS also provides an alternative method for endpoint detection with a potentially higher time resolution than by imaging. On the basis of the time evolution of in situ EELS spectra, a qualitative working model combining knock-on sputtering, irradiation-induced mass transport, and phase separation can be proposed.