Biomaterials often display outstanding combinations of mechanical properties thanks to their hierarchical structuring, which occurs through a dynamically and biologically controlled growth and self-assembly of their main constituents, typically mineral and protein. However, it is still challenging to obtain this ordered multiscale structural organization in synthetic 3D-nanocomposite materials. Herein, we report a new bottom-up approach for the synthesis of macroscale hierarchical nanocomposite materials in a single step. By controlling the content of organic phase during the self-assembly of monodisperse organically-modified nanoparticles (iron oxide with oleyl phosphate), either purely supercrystalline or hierarchically structured supercrystalline nanocomposite materials are obtained. Beyond a critical concentration of organic phase, a hierarchical material is consistently formed. In such a hierarchical material, individual organically-modified ceramic nanoparticles (Level 0) self-assemble into supercrystals in face-centered cubic superlattices (Level 1), which in turn form granules of up to hundreds of micrometers (Level 2). These micrometric granules are the constituents of the final mm-sized material. This approach demonstrates that the local concentration of organic phase and nano-building blocks during self-assembly controls the final material’s microstructure, and thus enables the fine-tuning of inorganic-organic nanocomposites’ mechanical behavior, paving the way towards the design of novel high-performance structural materials.