This study evidenced the nanoconfinement effect on polyphenolic extracts prepared from Salvia officinalis L. and Thymus serpyllum L. into the mesopores of silica and titania nanomaterials on their radical scavenging capacity and antimicrobial potential. The ethanolic and hydroalcoholic extracts obtained either by conventional or microwave-assisted extraction were characterized in terms of total polyphenols, total flavonoids, and chlorophyll content, as well as radical scavenging activity by consecrated spectrometric determinations. The phytochemical fingerprint of extracts was analyzed by high-performance liquid chromatography-photodiode array detector. Salvia officinalis extracts exhibited better radical scavenging capacity and antimicrobial potential than Thymus serpyllum extracts. The mesoporous MCM-41 silica and titania nanomaterials, prepared by the sol–gel method, were characterized by small- and wide-angle powder diffraction, FTIR spectroscopy, nitrogen adsorption–desorption isotherms, scanning electron microscopy and transmission electron microscopy, while the materials containing embedded extracts were analyzed through Fourier-transform infrared spectroscopy, N2 sorption measurements, and thermal analysis. All extracts free and embedded in mesoporous matrix exhibited high radical scavenger properties and good bactericidal activity against several reference strains. It was proved that by embedding the polyphenolic extracts into mesopores of silica or titania nanoparticles, the phytochemicals stability was enhanced as the materials containing extract exhibited higher radical scavenger activity after 3–6 months storage than that of the free extracts. Additionally, the extract-loaded material showed mild improved antimicrobial activity in comparison with the corresponding free extract.