In the present study, we report a new process for modifying cellulosic fabrics by using ionic liquids. To this aim, 1-methylimidazolium chloride propyltriethoxysilane and 1-pyridinium chloride propyltriethoxysilane salts were synthesised. Then, the cotton fabrics were treated with sols containing these salts by the pad-dry-cure process. Finally, the treated fabrics were impregnated in a diluted solution of HPF6 to perform the metathesis reaction. The morphology and chemical composition of treated and untreated fabrics were analysed by scanning electron microscopy, elemental analysis and infrared spectroscopy. The droplet shape analysis confirmed that the water repellency of the fabrics was significant after surface modification. The flame retardancy was also enhanced by using the PF6 anion. Thermogravimetric analysis was used to assess the thermal stability of these treated fabrics in air.