The article presents a very simple method of synthesis and application of a halogen and formaldehyde free, P, S and Si-containing flame retardant for the durable finishing of cotton fabric. The compound was obtained as a result of the thiol-ene click reaction. The compound was designed to have two functional groups: an alkoxysilyl group for cross-linking and binding to the cotton fabric, and a phosphate group to provide flame retardant properties. The flame retardant was applied to cotton fabric using the sol–gel method. According to the pyrolysis-combustion flow calorimetry (PCFC) technique, the use of the obtained silane for cotton treatment can reduce heat release rate (HRR) to almost 75% compared to the raw fabric. FT-IR analyses and SEM images indicate that impregnated cotton samples were covered with a layer of silanes. The SEM–EDS analysis confirmed successful modification of cotton fabrics. After 10 cycles of washing it was found that the created coatings are resistant to washing and retain their flame retardant properties.