The worldwide use of ionic liquids (ILs) is steadily increasing, and even though they are often referred to as “green solvents” they have been reported to be toxic, especially toward aquatic organisms. In this work, we thoroughly study two phosphonium ILs; octyltributylphosphonium chloride ([P₈₄₄₄]Cl) and tributyl(tetradecyl)phosphonium chloride ([P₁₄₄₄₄]Cl). Firstly, the critical micelle concentrations (CMCs) of the ILs were determined with fluorescence spectroscopy and the optical pendant drop method in order to gain an understanding of the aggregation behavior of the ILs. Secondly, a biomimicking system of negatively charged unilamellar liposomes was used in order to study the effect of the ILs on biomembranes. Changes in the mechanical properties of adsorbed liposomes were determined by quartz crystal microbalance (QCM) measurements with silica coated quartz crystal sensors featuring a polycation layer. The results confirmed that both ILs were able to incorporate and alter the biomembrane structure. The membrane disrupting effect was emphasized with an increasing concentration and alkyl chain length of the ILs. In the extreme case, the phospholipid membrane integrity was completely compromised.