The production of Flexible Electronic Devices (FEDs) by roll-to-roll large-scale manufacturing processes is a rapidly growing sector and the development of functional (inorganic and/or organic) thin layers onto flexible polymeric substrates represents one of the key issues for the low cost production of FEDs. However, the flexible substrates should meet advanced demands, as high optical transparency, high barrier properties and increased adhesion of the subsequent functional layers, which will have a major affect on their performance, efficiency and lifetime. Plasma treatment can be successfully employed for the improvement of the bonding structure and surface properties of flexible polymeric substrates. In this work, we report on the effect of Pulsed DC N⁺ ion bombardment using different ion energies, on the bonding structure, electronic and optical properties and surface nanotopography of Poly(Ethylene Terephthalate) (PET) substrates. For the investigation of the optical properties, we have used in-situ and real-time Spectroscopic Ellipsometry from the IR to Vis-farUV spectral region, in combination to advanced modeling procedures, whereas Atomic Force Microscopy has been employed for surface nanotopography investigation. As it has been found, the N⁺ bombardment leads to the appearance of new chemical bonds (C-N or C-O bonds in Φ-NH₂, Φ-NHR, C({double bond, long}O)-NHR, Φ-OH, or (C{double bond, long}O)-OH), as well as partial disappearing of the C-O bond of ester group, on a surface layer of PET.