The microstructure of the active material of Li‐ion batteries has a crucial influence on local ion‐transport processes but is not yet well characterized. Atom probe tomography (APT), a method combining sub‐nanometer spatial resolution with sub‐parts‐per‐thousand chemical resolution is well suited for 3 D microstructural characterization. Herein, the results of the characterization of lithium (nickel)manganese oxides [L(N)MO] with APT are presented. Structural and chemical defects of different dimensions such as the segregation of Na impurities to grain boundaries and the appearance of a Ni‐rich foreign phase are detected. Furthermore, a lamellar microstructure correlated to fluctuations in the local Li content was observed, and its influence on Li transport in the material is discussed. In defect‐free regions, the lattice planes of LMO are reconstructed for the first time, and the high spatial resolution of APT is revealed. Thus, the results demonstrate the potential of APT for the 3 D microstructural characterization of LMO.