Metal nanoparticles (NPs) functionalized with self-assembled monolayers (SAMs) of long alkanethiol ligands are subject to defects in the SAM structure due to the interplay between alkyl chain packing and the free volume available in space per ligand. We find via dissipative particle dynamics (DPD) simulations that hydrophobic contact between protruding acyl chains of phospholipids from lipid vesicles and exposed alkyl chains in SAM defects prompts NP insertion and that defects become sites for phospholipid extraction. Experiments show that AuNPs coated with cationic (11-mercaptoundecyl)trimethylammonium bromide, analogous to the models used for the simulations, attach to and acquire lipids from planar supported lipid bilayers, while AuNPs coated with anionic 11mercaptoundecanoic acid do not. Phospholipid extraction and the structure of the ligands inserted in bilayers collectively contribute to bilayer thinning at the site of NP insertion and bilayercurvature-dependent deformability, revealing how these typical engineered SAM-coated NPs interface with lipid-bilayer systems with potential biological consequences.