Various biomedical applications of biodegradable nanofibers are a hot topic, as evidenced by the ever-increasing number of publications in this field. However, as-prepared nanofibers suffer from poor cell adhesion, so their surface is often modified. In this work, active polymeric surface layers with different densities of COOH groups from 5.1 to 14.4% were successfully prepared by Ar/CO2/C2H4 plasma polymerization. It has been shown that adhesion and proliferation of mesenchymal stem cells (MSCs) seeded onto plasma-modified PCL nanofibers are controlled by the CO2:C2H4 ratio. At a high CO2:C2H4 ratio, a well-defined network of actin microfilaments is observed in the MSCs. Nanofibers produced at a low CO2:C2H4 ratio showed poor cell adhesion and very poor survival. There were significantly fewer cells on the surface, they had a small spreading area, a poorly developed network of actin filaments, and there were almost no stress fibrils. The maximum percentage of proliferating cells was recorded at a CO2:C2H4 ratio of 35:15 compared with gaseous environments of 25:20 and 20:25 (24.1 ± 1.5; 8.4 ± 0.9, and 4.1 ± 0.4%, respectively). Interestingly, no differences were observed between the number of cells on the untreated surface and the plasma-polymerized surface at CO2:C2H4 = 20:25 (4.9 ± 0.6 and 4.1 ± 0.4, respectively). Thus, Ar/CO2/C2H4 plasma polymerization can be an excellent tool for regulating the viability of MSCs by simply adjusting the CO2:C2H4 ratio.