Abstract Anion doping offers immense potential for tailoring material properties, but precise control over anion incorporation remains challenging due to complex synthesis and limitations in dopant detection. This study investigates F-ion intercalation within an infinite-layer NdNiO2+x /SrTiO3 superlattice using a two-step process. We employ advanced four-dimensional scanning transmission electron microscopy (4D-STEM) coupled with electron energy loss spectroscopy (EELS) to map the F distribution and its impact on the atomic and electronic structure. Our observations reveal a fluorination-induced geometric reconstruction of the infinite layer structure, resulting in a more distorted orthorhombic phase compared to the pristine perovskite. F-ion are primarily located at apical polyhedral sites, with some basal sites occupation in localized regions, leading to the formation of two distinct domains. These domains reflect a competition between polyhedral distortion and Nd displacement at domain interfaces. Interestingly, we observe an anomalous structural distortion where basal site anions are displaced in the same direction as Nd atoms, potentially linked to the partial basal site F-ion occupation. This coexistence of diverse structural distortions signifies a locally disordered F-ion distribution with distinct configurations. These findings provide crucial insights into the mechanisms of anion doping at the atomic level, contributing to the design of materials with tailored functionalities.