The vapor-phase deposition of triethoxy(octyl)silane and 1H,1H,2H,2H-perfluoroctyltriethoxysilane on silica substrates was studied at different temperatures (70 - 150 °C). An original combination of spectroscopic (13C and 29Si solid state NMR, FTIR), electrochemical (CV, EIS) and surface (surface free energy determinations, AFM) characterization techniques was adopted to shed light on the role played by the alkylsilane structure and deposition temperature on the resulting layer. As for the unfluorinated molecule, both wettability and ion permeability displayed a bell-shaped curve with respect to the functionalization temperature. Spectroscopic techniques showed similar trends in the functionalization degree and suggested the formation of oligomers/polymers covalently attached to the surface. 29Si NMR proved that higher functionalization temperatures increase lateral polymerization across the alkylsilane layer. Conversely, the wettability was almost invariant with the functionalization temperature for the fluorinated analogue. However, electrochemical and spectroscopic results had a significant dependence on the functionalization conditions, even more marked than for the unfluorinated alkylsilane. The higher thermal reactivity of fluorinated molecules led to vertical polymerization, as supported by very high water contact angles, diffusion components in EIS and a lower degree of covalent bonding with the surface. Optimal deposition conditions were identified at 100 and 90°C for the unfluorinated and fluorinated alkylsilane, respectively.