An un-cross-linked SBR-system filled with precipitated silica nanoparticles of radius ≈10 nm by mixing is studied as a function of the fraction of graftable matrix chains (140 kg mol-1) varying from 0% to 100%, for a low (ΦSi = 8.5 vol %) and high (16.7 vol %) silica volume fraction. The linear rheology in shear shows a strong impact of the grafting on the terminal flow regime, and a shift to longer relaxation times with increasing grafting. Simultaneously, the plateau modulus stays approximately constant for the low ΦSi, suggesting a link to the silica content. The microstructure of the silica is characterized by using a combination of transmission electron microscopy and small-angle X-ray scattering data. We apply a quantitative model of interacting aggregates, and determine the average aggregation number (decreasing from 160 to 30 with grafting), aggregate size (50 to 30 nm), and compacity (55% to 35%). While the linear rheology seems to be dominated by the matrix composition, both the mixing rheology and the structure display a saturation with increasing grafting fraction. A closer analysis of this effect indicates that a critical amount of grafting is needed to trigger structural evolution. To summarize, a quantitative study of complex nanocomposites with several features of industrial systems demonstrates that the grafting density can be used as a fine-tuning parameter of rheology and microstructure.