Organically modified silicates represent an excellent example of organic–inorganic hybrids in materials science. The routes to achieve incorporation of organic functionalities include grafting and co-condensation (one-pot synthesis). Compared with the grafting method, the advantage of one-pot synthesis manifests as the tunability of both mechanical and biological properties. Herein, we report a silsesquioxane–silica hybrid (SqSH) with dual functional groups (alkylammonium and methacrylate chains) synthesized by the hydrolytic co-condensation of one tetraethoxysilane and two alkoxysilanes. Successful co-condensation is validated by attenuated total reflection-Fourier transform infrared (ATR-FTIR), ²⁹Si nuclear magnetic resonance (²⁹Si NMR), and thermogravimetric analysis (TGA). 3-(Trimethoxysilyl)propyldimethyloctadecyl ammonium chloride (SiQAC), one of the three precursors, simultaneously serves as a structure-directing agent in the modified Stöber reaction, resulting in SqSH particles with structural hierarchy of both ordered lamellar structure and spherical morphology, as revealed by X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The SqSH particles bear tunable mechanical properties and, when incorporated into bis-GMA/TEGDMA resin, antimicrobial activities against Streptococcus mutans, Actinomyces naeslundii, and Candida albicans.