DLC:Si and DLC:N (diamond-like carbons doped with Si or N) functional layers in different configurations are deposited on polyurethane (PU) for bioengineering applications using CCP (capacitively coupled plasma) discharge generated in the PE CVD (plasma-enhanced chemical vapor deposition) system. Scanning electron microscopy (SEM) observations show that the obtained single and multilayers are continuous and well adherent to the substrates, but they differ in surface morphologies. DLC:Si layers form granular-like outer surfaces, while DLC:N ones a mosaic structure of plain areas. Topography analyses by atomic force microscopy (AFM) and optical profilometry reveal that Si-doped layers are characterized by significantly higher surface roughness (Ra ca. 5 nm) in comparison to N-doped layers (Ra ca. 0.3 nm) and also higher values of profile roughness parameter Rz (up to 32 μm vs. about 13 μm). Energy-dispersive X-ray spectroscopy (EDS) analysis indicates the homogenous chemical composition of the layers. DLC:N layers, are characterized by significantly higher polar component of surface free energy (up to ca. 5.0 mJ/m2). DLC:Si layers exhibit higher values of diiodomethane contact angle (up to ca. 90°) compared with DLC:N layers (up to ca. 55°). The attenuated total reflectance Fourier transform infrared spectroscopic measurements (ATR-FTIR) of the layers reveal that the addition of silicon to the DLC structure increases the content of terminal CHn bonds (n = 1, 2, 3) as well as beneficial Si–H and Si–CHn bonds, which significantly reduce the internal stresses in the layers. Both DLC:Si and DLC:N layers exhibit no cytotoxic effects using the human osteoblast-like cell line and human keratinocytes.