The composite system comprising mesoporous silica nanoparticle KIT-6 with I3ad symmetry and polyelectrolyte complex (κ-carrageenan/chitosan/κ-carrageenan) was utilized as a promising carrier for the effective delivery of quercetin. KIT-6 silica nanoparticles with sizes around 45 nm were synthesized and modified with amino groups by post-synthesis method. Quercetin was successfully loaded into the amino-modified KIT-6 silica by incipient wetness impregnation or by solid state method. The quercetin-loaded KIT-6NH2 particles were coated by a two-layer polymer complex of oppositely charged polysaccharides. All the materials were characterized by XRD, N2 physisorption, thermal gravimetric analysis, AFM and ATR FT-IR spectroscopy. In-vitro release profile of quercetin loaded formulations was studied in a phosphate buffer with pH = 6.8. Polymer coated KIT-6NH2 formulations prepared by both methods showed slower quercetin release compared to that from the uncoated ones. ATR-FT-IR spectroscopic data suggested weak interaction of quercetin with the NH2-KIT-6. Density functional modeling revealed some aspects of quercetin bonding to the functionalized carrier at molecular level. The binding of quercetin to the protonated amino-functionalized silica carrier via the carbonyl group of the drug is more than twice weaker than the binding to the neutral carrier, which allows to be released easily as could be observed experimentally. The cytotoxicity potential of the mesoporous carrier was studied in three human cell lines (HEK-293, HL-60 and HUT-78). A comparative evaluation of the cytotoxic effect of quercetin loaded system vs. free drug was investigated in HUT-78 cell line.