The surface properties of electrospun scaffolds can greatly influence protein adsorption and thus strongly dictate cell-material interactions. In this study, we aim to investigate possible correlations between the surface properties of argon, nitrogen and ammonia/helium plasma-functionalized polycaprolactone (PCL) nanofibers (NFs) and their cellular interactions by examining the protein corona patterns of the plasma-treated NFs as well as the cell membrane proteins involved in cell proliferation. As a result of the performed plasma treatments, PCL NFs morphology was preserved while wettability was improved profoundly after all treatments because of the incorporation of polar surface groups. Depending on the discharge gas, different types of groups are incorporated which influenced the resultant cell-material interactions. Argon plasma-functionalized PCL NFs, only enriched by oxygen-containing functional groups, were found to show the best cell-material interactions, followed by N2 and He/NH3 plasma-treated samples. SDS-PAGE and LC-MS clearly indicated an increased protein retention compared to non-treated PCL NFs. The nine proteins best retained on plasma-treated NF are important mediators of extracellular matrix interaction, illustrating the importance thereof for cell proliferation and viability of cells. Finally, 92 proteins that can be used to differentiate the different plasma treatments are clustered and subjected to a gene ontology study, illustrating the importance of keratinization and extracellular matrix organization.