Silicon (Si) nanoparticles were coated inflight with silver (Ag) atoms using a novel method to prepare multicomponent heterostructured metal-semiconductor nanoparticles. Molecular dynamics (MD) computer simulations were employed, supported by high-resolution bright field (BF) transmission electron microscopy (HRTEM) and aberration-corrected scanning transmission electron microscopy (STEM) with a resolution ≤0.1 nm in high angle annular dark field (HAADF) mode. These studies revealed that the alloying behavior and phase dynamics during the coating process are more complex than when attaching hetero-atoms to preformed nanoparticles. According to the MD simulations, Ag atoms condense, nucleate and diffuse into the liquid Si nanoparticles in a process that we term "inoculation", and a phase transition begins. Subsequent solidification involves an intermediate alloying stage that enabled us to control the microstructure and crystallinity of the solidified hybrid heterostructured nanoparticles.