We report on a novel assembly approach to fabricate ultrathin robust freely standing nanocomposite membranes. The materials are composed of a pre-cross-linked silk fibroin matrix with incorporated silica nanoparticles with silsesquioxane cores (POSS) or clay nanoplatelets. These reinforced silk membranes have enhanced mechanical properties as compared to traditional silk-based nanocomposites reported previously. Up to 6-fold and 8-fold increase in elastic modulus and toughness, respectively, were found for these nanocomposites. In contrast, traditional LbL-assembled nanocomposites showed only a 3-fold increase in mechanical strength. The silk nanocomposites obtained also revealed excellent optical transparency in the visible region especially if reinforced with POSS nanoparticles, which suggests their utility as low cost, nontoxic, and easily scalable reinforced biomaterials for mechanically demanding applications.