Relativistic electron beam accelerators (5 MeV, 0.1 A) can now be flown on spacecraft. Injection from low-Earth-orbit into the atmosphere makes it possible to perform active perturbation experiments in the 40–60 km altitude range. These include modification of the atmospheric electric potential structure over thunderstorm regions and the possible stimulation of high-altitude-lightning, as well as studies of relativistic electron precipitation effects on chemical reaction paths. In this paper, the initial stage of the beam injection process is simulated by a fully electromagnetic and relativistic Particle-in-Cell (PIC) code. The self-consistent implementation of electric charging of a spacecraft structure in an electromagnetic code is demonstrated, and beam propagation dynamics is explored for a range of beam to ambient plasma densities. It is shown that the combined effects of ambient plasma and beam self-fields may allow propagation in the ion-focused regime and that this regime primarily is expected for relativistic beams.