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Ionic liquids (ILs) have remarkable properties and applications in many areas of science. Phosphonium ILs have become important because of their unique chemical and thermal stabilities. The present work is focused on the synthesis, characterisation, physicochemical properties, and microbial toxicity assessment of phosphonium ILs bearing seven different fatty acid anions. The structures of the synthesised ILs were confirmed by 1H and 13C nuclear magnetic resonance (NMR) and FTIR spectroscopy. Physicochemical properties such as density and viscosity of pure ILs were measured at temperatures ranging from 298.15 to 313.15 K. The experimental density decreased, whereas the viscosity increased with an increasing number of carbon atoms in the anion. The derived properties were also found to be anion dependent. The thermal decomposition temperature was investigated by TGA. Subsequently, the toxicity profile of the ILs was determined for selected Gram positive and Gram negative bacteria and some species of fungi in terms of minimum inhibitory concentrations (MIC). The results show that the antimicrobial activities of the ILs are strongly related to the structures of the ILs, where an increase in toxicity was observed with increasing alkyl group chain length of the fatty acid anion.