In this work, we demonstrate how to extract electron energy loss spectra of metallic nano-particles from time-domain computations. Specifically, we employ the Discontinuous Galerkin Time-Domain (DGTD) method in order to model the excitation of individual metallic nano-spheres and dimers of spheres by a tightly focussed electron beam. The resulting electromagnetic fields that emanate from the particles act back on the electrons and the accumulated effect determines the electrons’ total energy loss. We validate this approach by comparing with analytical results for single spheres. For dimers, we find that the electron beam allows for an efficient excitation of dark modes that are inaccessible for optical spectroscopy. In addition, our time-domain approach provides a basis for dealing with materials that exhibit a significant nonlinear response.