The rational design of nanocomposite structures with specific functions in energy storage applications is a key requisite to increase energy and power density in electrical storage systems. Nanoscale characterisation tools are essential to achieve controlled syntheses of such well-defined interface structures in order to reveal structure-property relationships in functional nanocomposites. In the following, we report on the synthesis of iron (hydr)oxide nanoparticles homogeneously embedded into the walls of the three dimensional carbon network of mesoporous carbon CMK-3 via a mild one-step redox functionalisation. Depth profile Auger electron spectroscopy (DP-AES) and energy filtered transmission electron microscopy (EF-TEM) are applied to analyse elemental distribution profiles and location of the active components. The combination of the two analytical techniques provides a highly resolved spatial distribution of transition metal (hydr)oxide nanoparticles inside the carbon network. Functionalised porous carbon nanocomposites were tested for supercapacitor applications and the highest energy density of an iron oxide carbon composite is demonstrated. The iron (hydr)oxide contributes with a pseudocapacitance of 357 F g^-1 to the porous nanocomposite in a 6 M KOH electrolyte. An overall doubling of the specific capacitance of the active electrode material compared to the pristine CMK-3 is achieved.