Using low pressure plasma polymerization, nano-scaled oxygen-rich plasma polymer films (CO) were deposited onto pristine silicon wafers as well as on nitrogen-containing plasma polymer (CN) model surfaces. We investigate the influence of the nature of the substrate as well as a potential sub-surface effect emerging from the buried CO/CN interface, just nanometers below the surface. X-ray Photoelectron Spectroscopy and Time-of-Flight Secondary Ion Mass Spectrometry revealed two important phenomena that occurred during the deposition of the terminal CO layer: (1) a strong degree of oxidation, already for 1 nm nominal thickness, and (2) a gradual transition in chemical composition between the two layers, clearly indicating that effectively a vertical chemical gradient results, even when a two-step coating process was applied. Such terminal gradient film structures were used to study film stability in aqueous environments. Molecular rearrangements were scrutinized in the top-surface in contact with water and we found that the top-surface chemistry and wetting properties of the oxygen-rich termination layer matched those of thick CO reference coatings. Nevertheless, the adsorption of green fluorescent protein (GFP) was observed to be sensitive to the CO terminal layer thickness. Namely, an enhanced protein adsorption was observed for 1–2 nm thick CO layers on CN, whereas a significantly reduced protein adsorption was seen on ≥ 3 nm thick CO terminal layers. We conclude that both, surface and sub-surface conditions significantly affect protein adsorption as opposed to the traditional consideration of surface properties alone.