The combination of high spatial resolution and near-surface chemical information makes Auger electron spectroscopy (AES) a powerful tool for comprehensive surface analysis. The recent interest in lithium metal as an active material in lithium sulphur or lithium air batteries increases the demand for a thorough knowledge of the reactions happening at the electrode interface. Applying AES to the complex surfaces of batteries, however, requires a detailed understanding of the interactions occurring with the highly reactive materials during investigation, especially when using metallic lithium with its passivation layers formed even under glove box atmosphere. The article is focused on the influence of electron beam damage and residual gas under ultra-high vacuum conditions on the observations made. Immediate irradiation effects are shown to highly depend on electron dose leading to misinterpretation the surface composition and a non-sufficient stability of the sample. The results are further supported by coupled X-ray photoelectron spectroscopy (XPS) measurements that help to understand the beam induced phenomena. An improved output of the spectroscopic measurement could be achieved employing AES mappings. This allows an improved insight into the local distribution of different lithium compounds in the material surface and can also be applied to other battery active materials.