Understanding the surface chemistry and oxygen surface exchange activity in mixed conducting perovskite and related perovskite oxides is of great relevance in developing electrochemical devices. Mixed conducting Ruddlesden–Popper Lan+1NinO3n+1 phases (n = 1, 2 and 3) have been considered as promising electrodes for electrochemical energy conversion cells due to their layered structure allowing non-stoichiometric defect structures. This study focuses on a systematic investigation of the chemical composition of the outermost atomic surfaces of as-deposited and annealed epitaxial films of Lan+1NinO3n+1 (n = 1, 2 and 3). For both as-deposited and annealed films, the analysis of the outermost surface using low energy ion scattering shows preferential LaO-termination. The results also provide evidence of an associated Ni-enrichment below the outermost surface. These findings suggest significant atomic rearrangement occurs during deposition and subsequent annealing. To investigate the thermal stability of these films during deposition, further microstructural analysis was carried out by means of high-resolution scanning transmission electron microscopy, showing significant re-orientation of LaO layers after a post-annealing heat treatment. In thin films of n = 2, 3 phases, surface restructuring reduces the epitaxy of the films and hence any potential beneficial anisotropy in transport properties will be lost. Care must therefore be exercised in processing these materials for electrode applications.