In this research work, silica nanoparticles and silica-gentamicin nanostructured solution were synthesized by using the microwave-assisted synthesis, in basic medium, using two silane precursors (tetraethylorthosilicate and octyltriethoxysilane) and the antibiotic (gentamicin sulfate). The prepared materials were characterized through Fourier transform infrared (FTIR) spectroscopy, TGA analysis, transmission electron microscopy (TEM), and atomic force microscopy (AFM) to investigate the morphology and structure. Antimicrobial studies of the silica-gentamicin nanostructured solution versus silica nanoparticles were performed against Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli. FTIR spectra showed that the gentamicin has been loaded to the silica nanoparticles. AFM analysis showed that the morphology of the silica-gentamicin nanostructured solution has changed, and agglomerations of particles are present at the surface. Antimicrobial testing, performed using the diffusion method through spot inoculation, indicates that the silica-gentamicin nanostructured solution exhibited activity against the resistant strain. The obtained silica-gentamicin solution can be used as biochemical agent for the prevention and treatment of microorganisms which are deposited on different surfaces (e.g., glass, plastic, ceramic).