The reaction of amorphous Co–Zr films with Si(100) and SiO2 substrates has been investigated using in situ Rutherford backscattering spectrometry, Auger electron spectroscopy and x‐ray diffraction. For this purpose, CoxZr1-x (x=0.5 or 0.6) films were deposited on a substrate and annealed in vacuum or NH3. During annealing of an amorphous Co–Zr film on Si in vacuum at a temperature lower than 600 °C, Co reacts with Si, forming CoSi2 next to the substrate. Above 600 °C, the layer reacts completely with Si and the following structure develops: (ZrSi2+CoSi2)/CoSi2/Si. Annealing the same structure in NH3 above 600 °C causes two reactions to occur simultaneously: (i) CoSi2 formation at the film/substrate interface, and (ii) nitridation of the film surface, forming ZrN, which stops the diffusion of Si to the surface. It was found that a fraction of the CoSi2 grains was aligned with the Si(100) substrate, irrespective of the annealing ambient. This fraction increases with increasing annealing temperature. When annealing below 600 °C in NH3, an oxide layer between the surface nitride layer and the interface silicide layer develops, retarding the formation of the nitride and silicide layer. On SiO2 the situation is complex since Zr reacts with SiO2 above 600 °C, resulting in a ZrO2 toplayer with underneath a Co–Si layer after annealing in vacuum. In NH3 an oxygen‐containing layer between the substrate and the ZrN top layer is formed.