We report the structure-dependent effects of polyoxometalate (POM), a bioactive cluster material, on liposome collapse activity. Structure and lacunary state of POM were found to have a critical role to govern the efficiency and kinetics of the collapse of model cell membranes. Keggin-type POM demonstrated fast collapse activity, but with different efficiencies dependent on the lacunary state. Furthermore, an increase in POM size changed its kinetic properties, from fast to delayed activity. This kinetic transition is discussed in terms of the energy barrier during the collapse process.