Hollow MnFeO nanoparticles (NPs) with an average size of 15 nm are produced from the solid state reaction of FeO-MnO heterostructures. These heterostructures are synthesized through the seeded-growth of MnO crystal domains on the surface of hollow FeO NPs obtained by the nanoscale Kirkendall effect. FeO-MnO heterostructures are subsequently annealed at 500 °C, enough temperature to promote the interfusion of Fe and Mn ions, but without compromising the hollow geometry. MnFeO nanostructures are tested as anode in lithium-ion batteries (LIBs), delivering large lithium storage capacities and high-rate capabilities of 1054 mAh g at 0.1 A g and 369 mAh g at 5 A g. Additionally, hollow MnFeO NPs display long cycling stability, with a capacity up to 887 mAh g at 0.3 A g after 450 cycles. The excellent performance of hollow MnFeO NPs as anode for LIBs is associated with their crystal structure, composition, and the presence of carbonized ligands, which further promote electrical conductivity and buffer the volume changes during cycling. Additionally, the small particle size and hollow morphology improves the lithium kinetics, structural stability and cycling performance.