To increase energy density in lithium-ion batteries (LIBs), novel anode materials are considered based on conversion and alloying mechanisms as these typically possess far higher storage capacity than graphite, however, cyclability of these compounds is typically poor. To overcome these issues, ternary or ‘mixed’ compounds are considered. However, the degree of mixing is often overlooked. Here, Atomic layer deposition (ALD) is used to investigate the influence of the degree of mixing, composition and crystallinity of ZnO–SnO2 ternary materials as LIB anodes. Firstly, two different mixing nanostructures of thin-film ZnO–SnO2 electrodes are constructed: atomically intermixed films where the Zn, Sn and O are mixed at the atomic scale in a single amorphous layer, and nanolaminated films where the ZnO layer and SnO2 layers form a structure with well-defined interfaces. Secondly, by tuning the ratio of ZnO and SnO2, different compositions are obtained. Finally, when ZnO–SnO2 composite films are annealed post-deposition, these can be crystallized to form Zn2SnO4 films. The electrochemical performances of these different variations of ternary ZnO–SnO2 composites were investigated as anode materials in LIBs. This demonstrated the potential of ALD as a research tool in LIBs research and revealed the importance of atomic scale intermixing in these ternary oxides as anodes.