In this paper, we report our findings on the preparation of a film/alloy/substrate system with the use of a low-energy high-current electron beam (LEHCEB), as a result of sequential growth of molybdenum and chromium films on a zirconium substrate by magnetron sputtering. The system was produced in a single vacuum cycle, by cyclic growth of molybdenum film on a substrate and LEHCEB irradiation, followed by chromium film growth as a final step. We demonstrate that LEHCEB irradiation leads to the formation of Mo–Zr alloy consisting mainly of the high-temperature phase β-Zr. The alloy has the form of a layer 4.2 ± 0.9 μm in thickness, containing molybdenum-enriched regions. Such regions result from the formation of secondary phases: intermetallic compound Mo₂Zr and a solid solution of Zr in Mo.