AbstractBinary metal oxides are attractive anode materials for lithium-ion batteries. Despite sustained effort into nanomaterials synthesis and understanding the initial discharge mechanism, the fundamental chemistry underpinning the charge and subsequent cycles—thus the reversible capacity—remains poorly understood. Here, we use in operando X-ray pair distribution function analysis combining with our recently developed analytical approach employing Metropolis Monte Carlo simulations and non-negative matrix factorisation to study the charge reaction thermodynamics of a series of Fe- and Mn-oxides. As opposed to the commonly believed conversion chemistry forming rocksalt FeO and MnO, we reveal the two oxide series topotactically transform into non-native body-centred cubic FeO and zincblende MnO via displacement-like reactions whose kinetics are governed by the mobility differences between displaced species. These renewed mechanistic insights suggest avenues for the future design of metal oxide materials as well as new material synthesis routes using electrochemically-assisted methods.