The scope of this work is the comparative analysis in terms of grafting rate structure of the grafted layer, and wetting behavior of three series of silica nanoparticles modified with alkyltrimethoxysilanes by using conventional heating with and without acid catalysis, and microwave irradiation. A comprehensive characterization of the grafted layer by means of Fourier transform infrared (FTIR) microanalysis, and solid state NMR techniques has shown that microwave irradiation provokes a pronounced increase in the loading rate compared to conventional heating. This microwave effect is outstanding in the case of the reactions with methyltrimethoxysilane, because of the acceleration of the condensation rate. Moreover, solid state NMR spectra (Si-29 and C-13) strongly suggest structural differences in the grafted layer obtained by the two heating sources. The wetting behavior of the modified nanoparticles was studied, concluding that these changes in the structure of the grafted layer induced by the synthetic procedure do not determine the values of the dynamic water contact angles.