The report discusses the influence of pre-treatment of metal substrates with a high-intense pulsed ion beam on functional properties of subsequently deposited protective coatings. Austenitic stainless steel and the Zr-1%Nb alloy have been studied, which are used in the nuclear industry as structural materials. The following irradiation parameters have been applied: the accelerating voltage of 200 kV, pulse duration of 90 ns, and the energy density per pulse of 1.5 J/cm2. After irradiation, coatings of both Fe-Cr-Al and Al-Si-N systems have been deposited by magnetron sputtering. Then, both normal and accidental losses of coolant conditions for water-cooled nuclear reactors are simulated. Radiation damage was modeled using 400 keV protons with a current density of 0.667 μA/cm2and a fluence of 2.25∙1016 proton/cm2. The second modeling method was the hydrogenation of samples – 360 °C, pressure of 2 atm for 2 hours. After irradiating the coatings with protons or saturating them with hydrogen, high-temperature oxidation of the samples was carried out in air and steam at a temperature of 1000 °C for 180 seconds. Finally, the oxidized samples have been studied by scratch tests and subsequent investigations using scanning electron microscopy in order to understand the effect of the pre-treatment procedure.