The on-demand availability of nanomaterials with selected size and well-defined chemical/physical properties is of fundamental importance for their widespread application. We report two clean, rapid, and non-destructive approaches for nanoparticle (NP) size selection in centrifugal fields. The first exploits rate zonal separation in a high viscosity gradient. The second exploits selective sedimentation of NPs with different sizes. These methods are here applied to metallic nanoparticles (MNPs) with different compositions and surface chemistry, dispersed either in water or organic solvents. The approach is general and can also be exploited for the separation of NPs of any material. We selectively sort both Au and AgNPs with sizes in the 10–30 nm range, achieving chemical-free MNPs with low polydispersivity. We do not use solutes, thus avoiding contamination, and only require low centrifugal fields, easily achievable in benchtop systems.