In this work we present results of an new experiment related to low energy protons bombardments on nano-structured optical coatings. Multilayer structures protected by different capping layers have been fabricated and exposed to low energy protons (1 keV). The experimental parameters have been selected considering the potential application of the coatings to solar mission instrumentation. Future solar missions will investigate the Sun from very close distances and optical components are constantly exposed to low energy ion particles irradiation. The experiment was repeated fixing the proton flux while varying the total dose accumulated. Results show that physical processes occurred at the uppermost interfaces can strongly damage the structure.