Nanoscale multilayer coatings (NMCs) with different crystal structures are considered as capable of self-healing after radiation damage due to the recombination of vacancies and interstitials. This work is focused on a defect distribution study of NMCs based on Zr/Nb layers (25/25 nm and 100/100 nm) after proton irradiation. Coatings with a total thickness of 1.05 ± 0.05 µm were irradiated by 900-keV protons using a pelletron-type electrostatic accelerator with an ion current of 2 µA for durations of 60 min to 120 min. The influence of the irradiation effect was studied by X-ray diffraction analysis (XRD), glow discharge optical emission spectrometry (GD–OES), and Doppler broadening spectroscopy using a variable energy positron beam. The results obtained by these methods are compatible and indicate that defect concentration of Zr/Nb NMCs remains unchanged or slightly decreases with increasing irradiation time.