A simple, low-cost, and reproducible method for creating materials with even silver nanoparticles (AgNP) dispersion was established. Chitosan nanofibers with silica phase (CS/silica) were synthesized by an electrospinning technique to obtain highly porous 3D nanofiber scaffolds. Silver nanoparticles in the form of a well-dispersed metallic phase were synthesized in an external preparation step and embedded in the CS/silica nanofibers by deposition for obtaining chitosan nanofibers with silica phase decorated by silver nanoparticles (Ag/CS/silica). The antibacterial activity of investigated materials was tested using Gram-positive and Gram-negative bacteria. The results were compared with the properties of the nanocomposite without silver nanoparticles and a colloidal solution of AgNP. The minimum inhibitory concentration (MIC) of obtained AgNP against Staphylococcus aureus (S. aureus) ATCC25923 and Escherichia coli (E. coli) ATCC25922 was determined. The physicochemical characterization of Ag/CS/silica nanofibers using various analytical techniques, as well as the applicability of these techniques in the characterization of this type of nanocomposite, is presented. The resulting Ag/CS/silica nanocomposites (Ag/CS/silica nanofibers) were characterized by small angle X-ray scattering (SAXS), X-ray diffraction (XRD), and atomic force microscopy (AFM). The morphology of the AgNP in solution, both initial and extracted from composite, the properties of composites, the size, and crystallinity of the nanoparticles, and the characteristics of the chitosan fibers were determined by electron microscopy (SEM and TEM).