Abstract Composite membranes made from Nafion ionomer with nano phosphonic acid-functionalised silica and colloidal silica were prepared and evaluated for proton exchange membrane fuel cells (PEMFCs) operating at elevated temperature and low relative humidity (RH). The phosphonic acid-functionalised silica additive obtained from a sol–gel process was well incorporated into Nafion membrane. The particle size determined using transmission electron microscope (TEM) had a narrow distribution with an average value of approximately 11 nm and a standard deviation of ±4 nm. The phosphonic acid-functionalised silica additive enhanced proton conductivity and water retention by introducing both acidic groups and porous silica. The proton conductivity of the composite membrane with the acid-functionalised silica was 0.026 S cm −1, 24% higher than that of the unmodified Nafion membrane at 85 °C and 50% RH. Compared with the Nafion membrane, the phosphonic acid-functionalised silica (10% loading level) composite membrane exhibited 60 mV higher fuel cell performance at 1 A cm −2, 95 °C and 35% RH, and 80 mV higher at 0.8 A cm −2, 120 °C and 35% RH. The fuel cell performance of composite membrane made with 6% colloidal silica without acidic group was also higher than unmodified Nafion membrane, however, its performance was lower than the acid-functionalised silica additive composite membrane.