We fabricate site-controlled, ordered arrays of embedded Ga nanoparticles on Si, using a combination of substrate patterning and molecular-beam epitaxial growth. The fabrication process consists of two steps. Ga droplets are initially nucleated in an ordered array of inverted pyramidal pits, and then partially crystallized by exposure to an As flux, which promotes the formation of a GaAs shell that seals the Ga nanoparticle within two semiconductor layers. The nanoparticle formation process has been investigated through a combination of extensive chemical and structural characterization and theoretical kinetic Monte Carlo simulations.