Innovative nanostructures made of a high payload of fluorophores and superparamagnetic nanoparticles (NPs) have simply been fabricated upon self-assembling in a two-step process. The resulting hybrid supraparticles displayed a dense shell of iron oxide nanoparticles tightly attached through an appropriate polyelectrolyte to a highly emissive non-doped nanocore made of more than 105 small organic molecules. Cooperative magnetic dipole interactions arose due to the closely packed magnetic NPs at the nanoarchitecture surface, causing enhanced NMR transverse relaxivity. Large in vivo MRI T2 contrast was thus obtained with unusually diluted solutions after intravenous injection in small rodents. Two-photon excited fluorescence imaging could be performed, achieving unprecedented location resolution for agents combining both magnetic nanoparticles and fluorescence properties. Finally, TEM imaging of the sectioned mouse tissue succeeded in isolating the core-shell structures, which represents the first image of intact complex magnetic and fluorescent nanoassemblies upon in vivo injection. Such highly cohesive dual nanoarchitectures should open great horizons toward the assessment with high spatial resolution of the drug or labeled stem cell biodistribution.