Surface chemical functionalization is used in analytical tools to immobilize biomolecules that will capture a specific analyte and also to reduce the nonspecific adsorption. Silane monolayers are widely used to functionalize silica surfaces. Their interfacial properties are linked to the silane organization. Here, we study, by molecular dynamics simulations, the effects of silane molecule head-group charge, alkyl chain length, and surface coverage on the structure of silane monolayers. Four molecules are investigated: 3-aminopropyldimethylethoxysilane, n-propyldimethylmethoxysilane, octadecyldimethylmethoxysilane, and tert-butyl-11-(dimethylamino(dimethyl)silyl)undecanoate. The results suggest that, while long alkyl chains straighten out and adopt a more organized structure as surface coverage increases, the tilt angle of short chains is independent of surface coverage. Furthermore, in the case of long alkyl chains, a charged head-group seems to reduce the tilt angle to surface coverage dependence. The simulated alkyl chain tilt angles were qualitatively validated by infrared spectroscopy and X-ray photoelectron spectroscopy. Also, a hexagonal packing is observed in all of the monolayers but is more defined as surface coverage increases. The nematic order parameter suggests that this packing is governed by the parallel orientation of the first C–C bonds near the surface. So, even short alkyl chains, with a large tilt angle distribution, present a hexagonal packing.