The electron beam, during high-resolution transmission electron microscopy, was employed to induce a phase transition in La0.6Sr0.4CoO2.5 (LSC) from a brownmillerite ordering to an oxygen deficient perovskite structure. Prior to irradiation, a strongly alternating out-of-plane lattice parameter was observed, reflecting electrostatic interactions between AO and BO/BO2 planes in the brownmillerite ordering. During electron beam irradiation for one hour, the oxygen vacancy ordering vanished gradually, and a uniform cubic perovskite structure prevailed. To exclude beam-induced heating effects, in situ heating experiments were performed, revealing a stable brownmillerite ordering in the relevant temperature range (up to at least 500 °C). Thus, we conclude that the phase transition is caused by knock-on processes that affect oxygen vacancies in terms of a transition from structural vacancies toward extremely high concentrations of randomly distributed point defects in the ABO3 structure.