The synthesis of alloyed nanoparticles has been studied extensively; however, the formation mechanisms involved remain unclear. Here, we reveal the detailed formation mechanism of alloyed nanoparticles in a Pd-Ru system, using a semibatch polyol method in which the simultaneous rapid reduction of both precursors was assumed to be the critical mechanism. We employed a microflow reactor to realize rapid heating and cooling. A significant difference in the reaction rate between the two precursors was observed. Pd was reduced within seconds, but the reduction of Ru was 2 orders of magnitude slower than that of Pd and was not as rapid as previously assumed. Further investigation of the semibatch method was performed to trace changes in the particle sizes and composition. Through quantitative and multilateral evidence, we concluded that the formation of low-crystallinity seeds, followed by solid-state diffusion, is the governing mechanism for the formation of alloyed Pd-Ru nanoparticles.