Iron oxide nanomaterials are promising candidates for various electrochemical applications. However, under operating conditions high electric resistance is still limiting performance and lifetime. By incorporating the electronically conductive carbon into a nanohybrid, performance may be increased and degeneration due to delamination may be prevented, eliminating major drawbacks. For future applications, performance is an important key, but also cost-effective manufacturing suitable for scale-up must be developed. A possible approach that shows good potential for up-scale is magnetron sputtering. In this study, a systematic investigation of iron oxides produced by RF magnetron sputtering was carried out, with a focus on establishing correlations between process parameters and resulting structural properties. It was observed that increasing the process pressure was favourable with regard to porosity. Over the entire pressure range investigated, the product consisted of low-crystalline Fe3O4, as well as Fe2O3 as a minor phase. During sputtering, a high degree of graphitisation of carbon was achieved, allowing for sufficient electronic conductivity. By means of a new alternating magnetron sputtering process, highly homogeneous salt-and-pepper-type arrangements of both nanodomains, iron oxide and carbon were achieved. This nano-containment of the redox-active species in a highly conductive carbon domain improves the material’s overall conductivity, while simultaneously increasing the electrochemical stability by 44%, as confirmed by cyclic voltammetry.