The sol–gel route represents a valuable technique to obtain functional materials, in which organic and inorganic members are closely connected. Herein, four hybrid materials, containing caffeic acid entrapped in a silica matrix at 5, 10, 15, and 20 wt.%, were synthesized and characterized through Fourier-Transform Infrared (FT-IR) and Ultraviolet-Visible (UV–Vis) spectroscopy. FT-IR analysis was also performed to evaluate the ability to induce the hydroxyapatite nucleation. Despite some structural changes occurring on the phenol molecular skeleton, hybrid materials showed scavenging properties vs. 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and 2,2′-azinobis-(3-ethylbenzothiazolin-6-sulfonic acid) radical cation (ABTS•+), which was dependent on the tested dose and on the caffeic acid wt.%. The SiO2/caffeic acid materials are proposed as valuable antibacterial agents against Escherichia coli and Enterococcus faecalis.