The nanofiltration composite membranes were obtained by incorporation of KIT-6 ordered mesoporous silica, before and after its functionalization with amine groups, into polyphenylene-ether-ether-sulfone (PPEES) matrix. The incorporation of silica nanoparticles into PPEES polymer matrix was evidenced by FTIR and UV–VIS spectroscopy. SEM images of the membranes cross-section and their surface topology, evidenced by AFM, showed a low effect of KIT-6 silica nanoparticles loading and functionalization. The performances of the obtained membranes were appraised in permeation of <i>Chaenomeles japonica</i> fruit extracts and the selective separation of phenolic acids and flavonoids. The obtained results proved that the PPEES with functionalized KIT-6 nanofiltration membrane, we have prepared, is suitable for the polyphenolic compound’s concentration from the natural extracts.