The annealing of radiation damage in zircon by low-energy electron irradiation was explored systematically. Natural zircon samples spanning a wide range of self-irradiation damage were irradiated with the focused electron beam of an electron probe microanalyser. The effects of beam current and irradiation time were tested systematically, and the changes in zircon were measured using Raman spectroscopy. Our results confirm the damage-annealing effect of an accelerated electron beam. We demonstrate that non-thermal annealing occurs through electron-enhanced defect reactions and that the extent of the annealing is a function of both the irradiation time and the beam current. The complete annealing of radiation damage in zircon by an accelerated electron beam was not possible under the conditions of our experiments. Our results indicate that Raman band broadening in ion-irradiated zircon can possibly be explained through phonon confinement, as the estimated domain sizes of the crystalline volume amid recoil clusters decrease with increasing α dose. The results underlay the importance of doing Raman spectroscopy before electron-beam and ion-beam analysis. To avoid unwanted beam-induced annealing of damage in zircon during EPMA analysis, the electron energy transferred per volume unit of sample should be minimised, for instance by keeping the integrated charge low and/or by defocusing the electron beam.