Quartz crystal microbalance with dissipation (QCM-D) monitoring and atomic force microscopy (AFM) were combined to evaluate the defects created by an ionic liquid anion and a cation in a supported phospholipid bilayer composed of zwitterionic lipids on a silica surface. The cation 1-octyl-3-methyl imidazolium (OMIM+) was shown to remove lipids from the bilayer, increase the roughness to approximately 2.8 nm (similar to 0.2 for stable supported bilayer) and possibly redeposit lipids with entrapped water. The anion bis(trifluoromethylsulfonyl) imide (Tf2N-) was found to leave distinct defects within the bilayer that had large pore-like interiors which left the surrounding bilayer intact. However, the ionic liquid 1-butyl-1-methyl pyrrolidinium bis(trifluoromethylsulfonyl) imide (BMP-Tf2N) formed a film over the supported bilayer. This work demonstrates, for the first time, the direct effects common components of ionic liquids have on a supported phospholipids bilayer.