In this work, ionic liquids (ILs) containing the phosphonium cation and four different types of fluorous anions were synthesized and characterized with nuclear magnetic resonance spectroscopy, Fourier-transform infrared spectroscopy, elemental analyser (CHNS) and thermogravimetric techniques. The catalytic transesterification properties of the prepared ILs were investigated through the synthesis of biodiesel from waste cooking oil (WCO). The biodiesel synthesis was performed in two-step processes. Initially, the WCO was esterified with sulphuric acid to reduce its acid value (0.7 mg KOH/g). Later the transesterification reaction was carried out with the prepared ILs, and the process was optimized with respect to IL types, catalyst loading, methanol�oil ratios, temperature, agitation speed and time. Tetrabutylphosphonium bis(trifluoromethylsulfonyl)imide (TBPNTf2) was identified as a promising catalyst with the highest yield of biodiesel up to 81% at 4.5 wt% of IL loading, 18:1 ratio of methanol:WCO, 10 h of treatment time, 60 °C heating temperature and 600 rpm of agitation speed. The obtained product of biodiesel was characterized and analysed by different techniques, and its physicochemical properties were further determined using the known standard methods of American Society for Testing and Materials and European standards (ASTM and EN). © 2018, Islamic Azad University (IAU).