Cobalt nanoparticles were synthesised via the thermal decomposition of Co2(CO)8 and were coated in iron oxide using Fe(CO)5. While previous work focused on the subsequent thermal alloying of these nanoparticles, this study fully elucidates their composition and core@shell structure. State-of-the-art electron microscopy and statistical data processing enabled chemical mapping of individual particles through the acquisition of energy-filtered transmission electron microscopy (EFTEM) images and detailed electron energy loss spectroscopy (EELS) analysis. Multivariate statistical analysis (MSA) has been used to greatly improve the quality of elemental mapping data from core@shell nanoparticles. Results from a combination of spatially resolved microanalysis reveal the shell as Fe3O4 and show that the core is composed of oxidatively stable metallic Co. For the first time, a region of lower atom density between the particle core and shell has been observed and identified as a trapped carbon residue attributable to the organic capping agents present in the initial Co nanoparticle synthesis.