Magnetic nanoparticles have multiple applications in materials science. In particular, virus capsids have been suggested as promising templates for building up nanometric-sized magnetic clusters by taking advantage of their inner cavity as a nanoreactor. In this study we investigate the magnetization of individual cobalt-filled Cowpea mosaic virus empty virus-like particles using Atomic Force Microscopy. We also combine the analysis of the effects of dehydration on the structure of virus particles with a comparison of their magnetic signal to that provided by commercially available magnetic nanoparticles of similar size. These two approaches allow evaluation of the structure of the metallic cluster grown inside the virus capsid. We conclude that, rather than forming solid clusters, cobalt inside viruses forms a discontinuous structure which does not completely fill the viral cavity and reaches about 10% of its volume.