Silica–rubber nanocomposites were obtained by in situ sol–gel synthesis, using trialkoxysilanes with different functional groups as precursors. The functionalities were selected in order to favor the formation of differently shaped silica particles and/or to modulate the filler–filler and the filler–rubber interactions. The functional groups included (a) alkyl and alkenyl groups: triethoxy(vinyl) (VTEOS), triethoxy(propyl) (PTEOS), triethoxy (octyl) (OCTEOS); (b) N-containing alkyl groups: triethoxy(3-aminopropyl) (APTEOS), triethoxy(3- cyanopropyl) (CPTEOS), triethoxy(3-propylisocyanate) (ICPTEOS); (c) S-containing alkyl groups: trimethoxy(3-mercaptopropyl) (TMSPM), bis(3-triethoxysilylpropyl) disulfide (TESPD), bis(3-triethoxysilylpropyl) tetrasulfide (TESPT); triethoxy(3-octanoylthio-1-propyl) (NXT). Transmission electron microscopy (TEM) investigation suggested a relationship between the morphology of the filler network and the used trialkoxysilanes, as a function of the particle shape and of the interaction of the particle surface groups between them and with the matrix. The dynamic-mechanical properties of nanocomposites, both uncured and vulcanized, were discussed in relation to the network morphology, suggesting a connection between the used silica precursors and the functional properties. The filler–rubber interaction due to substituents which chemically interact with the polymer, promotes the homogeneous distribution of the silica particles in the matrix, while the filler–filler interaction, favored by the shape induced physical interactions or by the chemical interaction among surface groups, mainly contribute to the filler networking and to the dynamic-mechanical properties of the composites.