AbstractThe use of scanning transmission electron microscopes to manipulate substitutional defects in graphene has recently been demonstrated and modeled using ground state molecular dynamics, but the role of electronic excitations induced through inelastic electron scattering in promoting these transformations has so‐far remained unexplored. Here, probed are the effects of electronic excitation on the structural dynamics of graphene quantum dots of differing edge morphologies that are substitutionally doped with silicon or phosphorous. The ground and excited state potential energy barriers for pyramidal inversion of these nonplanar doped species are evaluated using time‐dependent density functional theory. Optically bright excited states in which the barrier is decreased are identified in the low energy region of the electronic spectrum, suggesting that photoexcitation can modulate the reactivity of defects in graphene under electron beam irradiation. Coupling matrix elements between these inversion‐favoring excited states and the ground state and time‐domain simulations of the material's response to a point charge impulse indicate that focusing an electron beam near the defect can also lead to population of these states, suggesting that beam electrons incident on a defect can both excite the material to an inversion‐favoring state and transfer momentum to the defect to initiate the inversion.