We investigated low temperature formation of a 10 nm thick amorphous Ni–Si layer after room temperature deposition of a 7 nm Ni layer on [001] Si, by in situ transmission electron microscopy analyses. Instead of a conventional time sequence of phases or an immediate formation of NiSi2 domains, annealing at 220 °C promotes Ni diffusion through a thin interfacial amorphous layer, formed during deposition, into the Si lattice until the entire supply of pure Ni atoms is consumed. High concentration nickel diffusion induces a crystalline-to-amorphous transformation of the original silicon lattice. Further increasing the temperature, in the range between 300 and 350 °C, causes crystalline NiSi2 domains to nucleate and grow within the amorphous matrix.