Ruthenium thin films were deposited by plasma-enhanced atomic layer deposition (PEALD) technology using Ru(EtCp)2 and oxygen plasma on the modified surface of silicon and SiO2/Si substrates. The crystal structure, chemical composition, and morphology of films were characterized by grazing incidence XRD (GXRD), secondary ion mass spectrometry (SIMS), and atomic force microscopy (AFM) techniques, respectively. It was found that the mechanism of film growth depends crucially on the substrate temperature. The GXRD and SIMS analysis show that at substrate temperature T = 375 °C, an abrupt change in surface reaction mechanisms occurs, leading to the changing in film composition from RuO2 at low temperatures to pure Ru film at higher temperatures. It was confirmed by electrical resistivity measurements for Ru-based films. Mechanical stress in the films was also analyzed, and it was suggested that this factor increases the surface roughness of growing Ru films. The lowest surface roughness ~1.5 nm was achieved with a film thickness of 29 nm using SiO2/Si-substrate for deposition at 375 °C. The measured resistivity of Ru film is 18–19 µOhm·cm (as deposited).