Sr2FeO3F, an oxyfluoride compound with an n = 1 Ruddlesden-Popper structure, was identified as a potential interesting mixed ionic and electronic conductor (MIEC). The phase can be synthesized under a range of different pO2 atmospheres, leading to various degrees of fluorine for oxygen substitution and Fe4+ content. A structural investigation and thorough comparison of both argon- and air-synthesized compounds were performed by combining high-resolution X-ray and electron diffraction, high-resolution scanning transmission electron microscopy, Mössbauer spectroscopy, and DFT calculations. While the argon-synthesized phase shows a well-behaved O/F ordered structure, this study revealed that oxidation leads to averaged large-scale anionic disorder on the apical site. In the more oxidized Sr2FeO3.2F0.8 oxyfluoride, containing 20% of Fe4+, two different Fe positions can be identified with a 32%/68% occupancy (P4/nmm space group). This originates due to the presence of antiphase boundaries between ordered domains within the grains. Relations between site distortion and valence states as well as stability of apical anionic sites (O vs F) are discussed. This study paves the way for further studies on both ionic and electronic transport properties of Sr2FeO3.2F0.8 and its use in MIEC-based devices, such as solid oxide fuel cells.