We have performed NH3 plasma treatment of poly(ethylene-2,6-naphthalate) (PEN) surfaces with the purpose of incorporating nitrogen functional groups. X-Ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion spectroscopy (ToF-SIMS) were used to determine changes in the chemical structure of the PEN surfaces in response to different levels of plasma power. Plasma power had a significant impact on the type of nitrogen functional groups as well as the level of nitrogen incorporation. Considerable degradation and oxidation occurred with an excessive plasma power, rather than nitrogen incorporation. Optical emission spectroscopy (OES) confirmed that the type of chemical species present in the plasma discharge primarily determines the surface functionality with the plasma treatment. Partially decomposed ammonia species (NH and NH2) are considered to react with the PEN surface and form primarily amine groups. However, stable N2 species produced by bimolecular combination of fully decomposed atomic species led to the formation of imine groups via atomic rearrangement. Moreover, ion bombardment by N2 + species adversely affected the chemical structure of the surface, resulting in degradation of ester and carbon-carbon bonds and surface etching of carbon atoms.