This paper describes the study of the structural properties of the alloy layers prepared by two different, impulsively working PAPVD methods: the Pulsed Magnetron Sputtering (PMS) and the Impulse Plasma Deposition (IPD). The Fe–Cu alloy layers were synthesized. The results of our investigation revealed a nanocrystalline structure of the layers. The differences in the phase composition of the Fe–Cu alloy layers produced by these two methods were observed. The synthesis of the Fe–Cu layers by using the Pulsed Magnetron Sputtering method resulted in obtaining the two-phase, polycrystalline structures (fcc-Cu and bcc-Fe). In this case the clear evidence of mixing between the iron and copper atoms was not observed. The Fe–Cu layers deposited by the Impulse Plasma Deposition method were characterized by the non-equilibrium phase composition – the presence of one-phase supersaturated solid solution (fcc-Cu(Fe) or bcc-Fe(Cu)) was formed in immiscible systems. These results suggest a short-distance diffusion between the neighboring nanoparticles of the two metals (Cu and Fe) occurring during the IPD layers growth.