Owing to their unique properties and unlimited structural combinations, the ubiquitous use of ionic liquids (ILs) is steadily increasing. The objective of the present work is to shed light onto the effects of amidinium- and phosphonium-based ILs on phospholipid vesicles using a nanoplasmonic sensing measurement technique. A new and relatively simple method was developed for the immobilization of large unilamellar vesicles on two different hydrophilic surfaces composed of titanium dioxide and silicon nitride nanolayers. Among the pretreatment conditions studied, vesicle attachment on both substrate materials was achieved with HEPES buffer in the presence of sodium hydroxide and calcium chloride. To get an understanding of how ILs interact with intact vesicles or with supported lipid bilayers, the ILs 1,5-diazabicyclo(4.3.0)non-5-enium acetate ([DBNH][OAc]), tributyl(tetradecyl)phosphonium acetate ([P14444][OAc]), and tributylmethylphosphonium acetate ([P4441][OAc]) were introduced into the biomimetic system, and the characteristics of their interactions with the immobilized vesicles were determined. Depending on the IL, in situ real-time IL binding and/or phospholipid removal processes were observed. Although [DBNH][OAc] did not have any significant effect on the phospholipid vesicles, the strongest and the most significant effect was observed with [P14444][OAc]. The latter caused clear changes in the phospholipid bilayer: the ILs interacted with the bilayers, resulting in deformation of the vesicles most probably due to the formation of vesicle - IL aggregates. Only a mild effect was observed when [P4441][OAc], at a very high concentration, was exposed to the intact vesicles. In general, these results led to new insights into the effects of ILs on phospholipid vesicles, which are of great importance to the overall understanding of the harmfulness of ILs on biomembranes and biomimicking systems. In addition, the present work highlights the pivotal role of this highly surface-sensitive indirect biosensing technique in scrutinizing and dissecting the integrity and architecture of phospholipid vesicles in the nanoscale range. (Figure Presented).