A series of phosphonium amphiphilic compounds was synthesized. Cationic parts of molecules contain triphenylphosphonium moieties. Lipophilic parts of compounds are represented by straight alkyl chain or the alkyl chains which are ornamented by benzyl or metronidazole. The physicochemical properties of phosphonium amphiphilic compounds were investigated by the measurements of surface tension and conductivity. The critical micelle concentration (cmc), the surface tension value at the cmc (γ cmc), the surface area at the surface saturation per head group (A cmc) were determined. The lowest cmc value was determined for phosphonium salts with straight dodecyl alkyl chain. Its value was 1.5 × 10 −3 mol dm −3. Surface tension at the cmc decreases with the addition of bulky moieties (benzyl, radical from metronidazol) at the end of alkyl chains. Biological activities of compounds were studied on human erythrocytes and strains of Acanthamoeba lugdunensis and Acanthamoeba quina. Dodecyltriphenylphosphonium bromide showed the highest activity against Acanthamoeba. To the best of our knowledge, it is the first compound of the group of phosphonium amphiphiles, which exhibited high activity against Acanthamoeba. The determined structure-activity relationship indicated nonspecific trophocidal and hemolytic activity that depends on physicochemical properties of the studied compounds.