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The crystal structure of BaFe0.9In0.1O3−δ, which was prepared via heating in N2 (BFI010‐N2), was evaluated using high‐temperature X‐ray diffraction (XRD) and in situ convergent‐beam electron diffraction (CBED) at room temperature and 700°C. Although the crystal structure of BFI010‐N2 at room temperature was assigned to a cubic perovskite‐type structure based on the XRD results, the CBED patterns indicated that the space group of its crystal structure was not Pm3¯m (No. 221), which corresponds to an ideal cubic perovskite. When the temperature was increased to 700°C, the symmetries for the space group of cubic perovskite were directly observed by means of in situ CBED, indicating that the partial ordering and/or clustering of oxide ion vacancies in the BFI010‐N2 vanished and that the oxide ion vacancy arrangements became completely random. The change in crystal symmetry agreed with a sudden decrease in the activation energy of oxide ion conduction at 600°C. The crystal symmetry of the BaFe0.9In0.1O3−δ sample that was prepared via heating in O2 (BFI010‐O2) and had a decreased δ value was compared with that of the BFI010‐N2 sample. It was concluded that the same phase transition also occurred by a decrease in δ, similar to phase transitions caused by increasing the temperature.