Heterogeneous gas-phase condensation is a promising method of producing hybrid multifunctional nanoparticles with tailored composition and microstructure but also intrinsically introduces greater complexity to the nucleation process and growth kinetics. Herein, we report on the synthesis and growth modeling of silicon–silver (Si–Ag) hybrid nanoparticles using gas-aggregated cosputtering from elemental Si and Ag source targets. The final Si–Ag ensemble size was manipulated in the range 5–15 nm by appropriate tuning of the deposition parameters, while variations in the Si–Ag sputtering power ratio, from 1.8 to 2.25, allowed distinctive Janus and core–satellite structures, respectively, to be produced. Molecular dynamics simulations indicate that the individual species first form independent clusters of Si and Ag without significant intermixing. Collisions between unlike species are unstable in the early stages of growth (<100 ns), with large temperature differences resulting in rapid energy exchange and separation. Upon further cooling and depletion of isolated Si and Ag atoms through collection by parent clusters (>100 ns), Si–Ag cluster collisions ultimately result in stable hybrid structures.