It is well known that flavonoids can chelate transition metals. Flavonoid-metal complexes exhibit a high antioxidative and therapeutic potential. However, the complexes are frequently hydrophobic ones and low soluble in water, which restricts their medical applications. Integration of these complexes into liposomes may increase their bioavailability and therapeutic effect. Here, we studied the interaction of quercetin-iron complexes with dimyristoylphosphatidylcholine (DMPC) or palmitoyl-oleoyl phosphatidylethanolamine (POPE) multilamellar liposomes. Differential scanning calorimetry (DSC) and freeze-fracture electron microscopy revealed that quercetin-iron complexes did not interact with liposomes. Quercetin however could penetrate lipid bilayers, when added to liposomes at a temperature above lipid melting. Iron cations added later penetrated into the lipid bilayers and produced complexes with quercetin in the liposomes. The quercetin-iron entry in POPE liposomes was improved when the suspension was heated above the temperature of the bilayer-hexagonal HII phase transition of the lipid. The approach proposed facilitates the integration of quercetin-iron complexes into liposomes and may promote their use in medicine.