The cytotoxicity of ionic liquids (ILs) has been receiving attention in the context of the biological and environmental impact of their vast field of applications. It has been ascertained that the cell membrane is the main target of ILs when they interact with microorganisms, cells and bacteria; nevertheless, studies at the micro- and nano-scale aiming at better understanding of the fundamental mechanisms of toxicity of ILs are lacking. In this work, we used atomic force microscopy (AFM) to investigate the impact of room-temperature ILs on the mechanical, morphological and electrostatic properties of solid-supported DOPC phospholipid bilayers, taken as models of biomembranes. In particular, we have characterized the concentration-dependent and time-dependent evolution of the morphological, structural and mechanical properties of DOPC lipid membranes in the presence of imidazolium-based ILs with different alkyl chain lengths and hydrophilic/hydrophobic characteristics. The majority of ILs investigated were found to possess the ability of restructuring the lipid bilayer, through the formation of new IL/lipid complexes, showing distinctive morphological features (increase of area and roughness). The nanomechanical analysis of the lipid membrane exposed to ILs revealed a progressive, concentration-dependent perturbation of the structural ordering and rigidity of the membrane, evidenced by a decrease in the breakthrough force, Young's modulus and area stretching modulus. AFM detected a modification of the electrostatic double-layer at the membrane surface, in terms of a reduction of the original negative surface charge density, suggesting a progressive stratification of cations on the exposed leaflet of the lipid membrane. Our findings may be helpful in designing novel ILs with tailored interaction with biological membranes.