In the present paper we have demonstrated how the change of the layer by layer deposition parameters can influence the final properties of cotton fabrics in terms of coating morphology, thermal stability and flammability. To this aim, novel synthetized oligoallylamines and phosphonated oligoallylamines have been assembled on the surface of cotton exploiting different molecular weights and pH conditions. Low molecular weights have yielded an incomplete “island growth” coating while high molecular weight resulted in a homogeneous coating which thickness was controlled by the adopted pH. Both low and high molecular weight assemblies induced a reduction of the cellulose decomposition temperatures that was, conversely, delayed by coatings assembled at pH=10. All assemblies were able to improve cotton flammability by suppressing the afterglow phenomenon; the best results in terms of flame spread and final residue have been achieved by high molecular weight assemblies.