The conformation of poly(ethyl methacrylate) chains in silica–latex nanocomposites has been studied under zero average contrast conditions (ZAC) using small-angle neutron scattering (SANS). Samples have been prepared by drying colloidal suspensions of silica and polymer nanoparticles (NPs) followed by thermal annealing, for two different silica NPs (radius of 5 and 15 nm) and two chain molecular weights (17 and 100 kg/mol). By appropriate mixing of hydrogenated and deuterated polymer, chain scattering contrast is introduced, and in principle silica scattering suppressed. The silica structure consisting mostly of small fractal aggregates is characterized by transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) on the same samples. The measurement of the chain structure by SANS, however, is perturbed by unwanted silica contributions, as often reported in the literature. Here, the contribution of contrast-matched silica is evidenced as a function of system parameters, namely chain mass, silica size, and volume fraction, and a model rationalizing these contributions for the first time is proposed. On the basis of a statistical analysis, a nanometer-thick polymer shell surrounding silica NPs is shown to create contrast, which is presumably maintained by the reduced mobility of polymer close to interfaces or attractive polymer–silica interactions. This shell is proven to be quantitatively important only for the smallest silica NPs. Finally, the pure polymer scattering can be isolated, and the polymer radius of gyration is found to be independent of filler content and NP size.