In this paper, the sol-gel technique was used to design hybrid phosphorus-doped silica structures for improving the thermal stability and flame retardancy of cotton fabrics. To this aim, diethylphosphatoethyltriethoxysilane (DPTS) was employed as phosphate alkoxysilane in a multistep procedure that involved multiple layers (from 1 to 6) depositions. The multi-layer coatings were applied by padding using sols containing appropriate molar ratios of the precursor, anhydrous ethanol, catalyst, and hydrochloric acid. Moreover, the synergism P-N on flame retardancy of cotton was assessed by introducing 3-aminopropyltriethoxysilane (APTES) as an N-donor precursor in DPTS sols. The effects of the catalyst during the alkoxide reaction and the silica amount applied by sol-gel treatment on the thermo-oxidative behavior of the treated fabrics were deeply studied. The creation of the silica skeleton on the cotton surface and the interactions between the cellulosic fibres and the doped layer were investigated using FT-IR ATR spectroscopy. Moreover, thermal and thermo-oxidative stability, flammability properties, and combustion behavior of the sol-gel treated cotton fabrics were also studied, proving the effectiveness of the sol-gel coating in the fire protection of the cellulosic substrate.