LiMn2O4 is a promising candidate for a cathode material in lithium-ion batteries because of its ability to intercalate lithium ions reversibly through its three-dimensional manganese oxide network. One of the promising techniques for depositing LiMn2O4 thin-film cathodes is atomic layer deposition (ALD). Because of its unparalleled film thickness control and film conformality, ALD helps to fulfill the industry demands for smaller devices, nanostructured electrodes, and all-solid-state batteries. In this work, the intercalation mechanism of Li+ ions into an ALD-grown β-MnO2 thin film was studied. Samples were prepared by pulsing LiOtBu and H2O for different cycle numbers onto about 100 nm thick MnO2 films at 225 °C and characterized with X-ray absorption spectroscopy, X-ray diffraction, X-ray reflectivity, time-of-flight elastic recoil detection analysis, and residual stress measurements. It is proposed that for <100 cycles of LiOtBu/H2O, the Li+ ions penetrate only to the surface region of the β-MnO2 film, and the samples form a mixture of β-MnO2 and a lithium-deficient nonstoichiometric spinel phase LixMn2O4 (0 < x < 0.5). When the lithium concentration exceeds x ≈ 0.5 in LixMn2O4 (corresponding to 100 cycles of LiOtBu/H2O), the crystalline phase of manganese oxide changes from the tetragonal pyrolusite to the cubic spinel, which enables the Li+ ions to migrate throughout the whole film. Annealing in N2 at 600 °C after the lithium incorporation seemed to convert the films completely to the pure cubic spinel LiMn2O4.