Silk fibroin (SF) is a versatile material with biodegradable and biocompatible properties, which make it fit for broad biomedical applications. In this context, the incorporation of nanosized objects into SF allows the development of a variety of bionanocomposites with tailored properties and functions. Herein, we report a thorough investigation on the design, characterization, and biological evaluation of SF hydrogels incorporating gold, silver, or iron oxide nanoparticles. The latter are synthesized in aqueous media using a biocompatible ligand allowing their utilization in various biomedical applications. This ligand seems to play a pivotal role in nanoparticle dispersion within the hydrogel. Results show that the incorporation of nanoparticles does not greatly influence the mechanism of SF gelation and has a minor impact on the mechanical properties of the so-obtained bionanocomposites. By contrast, significant changes are observed in the swelling behavior of these materials, depending on the nanoparticle used. Interestingly, the main characteristics of these bionanocomposites, related to their potential use for biomedical purposes, show the successful input of nanoparticles, including antibacterial properties for gold and silver nanoparticles and magnetic properties for iron oxide ones.