Recent results on synthesis, structural, and physicochemical studies of complexes based on detonation nanodiamonds modified with metal-organic molecules with functional magnetic and fluorescent properties have been presented. Neutron scattering experiments have discovered subtle features of the assembly of electro-negative molecules of Eu diphthalocyanines and nanodiamonds with positive surface potential in aqueous media. Nanoscale ordering of diamonds reinforced by their linking via diphthalocyanines was confirmed by TEM. The stable complexes possess X-ray luminescent and magnetic properties. Such nanostructures with low toxicity are prospective as contrasting and photoactive agents for magnetic resonance imaging and photodynamic therapy.