We show that assembled domains of magnetic iron-oxide nanoparticles (IONPs) are effective at increasing the dielectric permittivity of polydimethylsiloxane (PDMS) nanocomposites in the GHz frequency range. The assembly has been achieved by means of magnetophoretic transport and its efficacy, as well as the electromagnetic properties of the nanocomposite, has been found to depend on IONPs diameter. Remarkably, the dielectric permittivity increase has been obtained by keeping dielectric and magnetic losses very low, making us envision the suitability of nanocomposites based on aligned IONPs as substrates for radiofrequency applications.