Lipid coating is a method highly used to improve the biocompatibility of nanoparticles (NPs), even though its effect on the NP properties is still object of investigation. Herein, silica NPs containing methylene blue, which is a photosensitizer used in a variety of biomedical applications, were coated with a phospholipid bilayer. Regarding the photophysical properties, lipid-coating did not cause significant changes since bare and lipid-coated NPs presented very similar absorption spectra and generated singlet oxygen with similar efficiencies. However, NP interaction with cells and membrane mimics was totally different for bare and lipid-coated NPs. Lipid-coated NPs were distributed through the cell cytoplasm whereas bare NPs were detected only in some vacuolar regions within the cells. Since cellular uptake and cytolocalization are influenced by NP adsorption on cell membranes, the interaction of lipid-coated and bare NPs were studied on a membrane mimic, i.e., Hybrid Bilayer Membranes (HBMs) made of different compositions of negatively charged and neutral lipids. Interactions of bare and lipid-coated NPs with HBMs were analyzed by Surface Plasmon Resonance Imaging. Bare NPs presented high adsorption and aggregation on HBMs independently of the surface charge. Conversely, lipid-coated NPs presented less aggregation on the membrane surface and the adsorption was dependent on the charges of the NPs and of the HBMs. Our results indicated that NPs aggregation on the membrane surface can be modulated by lipid coating, which affects the cytosolic distribution of the NPs.