Organic–inorganic hybrid materials were synthesized by a sol–gel route, using silicon alkoxide together with low molecular weight polycaprolactone and caffetannic acid. The synthesized hybrids were characterized by scanning Fourier-transform infrared (FTIR) spectroscopy, and their surface morphology was acquired by scanning electron microscopy (SEM) analysis. The hybrids were investigated for their antiradical capacity using the DPPH and ABTS tests, while the Kirby–Bauer test was used to evaluate their effects on the growth of Escherichia coli and Enterococcus faecalis. Furthermore, a biologically active hydroxyapatite layer has been observed to form on the surface of intelligently synthesized materials. The MTT direct test showed that the hybrid materials are biocompatible with NIH-3T3 fibroblast cells, while they were cytotoxic towards colon, prostate, and brain tumor cell lines. These results shed new light on the suitability of the synthesized hybrids in the medical field, thus affording knowledge on the features of the bioactive silica–polycaprolactone–chlorogenic acid hybrids.