Although quercetin has a wide range of applications due to its biological properties, its activity may be affected due to its low solubility and its potential for degradation in a physiological environment. The nanoparticulate and microparticulate systems appear as a powerful strategy to enhance its biological activity as well as to contribute to the viability of this compound for pharmacological purposes. Here, we present an innovative and applied research to study theeffect of different lipid compositions on the encapsulation of quercetin by using multilamellar vesicles (MLVs). For this purpose, the effects of charge and rigidity in the formulation’s average size, size distribution, charge properties,encapsulation and release efficiencies of this polyphenol were explored. Our results demonstrated that the rigidity imposed by cholesterol increased both the homogeneity of the size distribution and the encapsulation efficiency enabling asignificant rate of quercetin release at the system with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/cholesterol (80:20). The charge modulated both the average size and size distribution as well as resulted in high encapsulation and release efficiencies in the formulation composed by (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2- oleoyl-sn-glycero-3-phosphatidylglycerol (80:20). To the best of our knowledge, this is the first study concerning chargeand rigidity effects on the encapsulation of quercetin in MLVs. Furthermore, the findings presented in this work is a starting point on the use of lipid composition as a modulating agent of important parameters in the development of nanoand micro systems for controlled release.