The effect of three phosphonium and imidazolium ionic liquids (ILs) on the interaction between liposomes and common pharmaceuticals found in wastewaters was studied. The liposomes comprised zwitterionic phosphatidyl choline and negatively charged phosphatidyl glycerol. A set of common cationic, anionic, and neutral compounds with varying chemical composition and unique structures were included in the study. The electrophoretic mobilities of the analytes were determined using conventional capillary electrophoresis (CE), using CE under reversed electroosmotic flow mobility conditions, and in the presence of ILs in the background electrolyte (BGE) solution by electrokinetic chromatography (EKC). In order to evaluate the impact of ILs on the interaction between the compounds and the liposomes, EKC was performed with liposome dispersions, with and without ILs. The retention factors of the compounds were calculated using BGEs including liposome dispersions with and without ILs. Two phosphonium based ILs, namely tributyl(tetradecyl)phosphonium chloride ([P14444]Cl) and octyltributylphosphonium chloride ([P8444]Cl), were chosen due to their long alkyl chains and their low aggregation concentrations. Another IL, i.e. 1-ethyl-3-methylimidazolium acetate ([emim][OAc]), was chosen based on our previous study, which suggests that it has a minimal or even nonexistent effect on liposomes at the used concentrations. The results indicate that the studied ILs have an effect on the interactions between wastewater compounds and liposomes, but the effect is highly dependent on the concentration of the IL and on the IL alkyl chain lengths. Most of the ILs hindered the interactions between the liposomes and the compounds, indicating strong interaction between ILs and liposomes. In addition, the nature of the studied compounds themselves affected the interactions.