Silylation of epoxidized soybean oil (ESBO) was carried out by epoxy ring opening reaction of methoxy and ethoxy silane compounds. $^{1}$H NMR and FTIR spectra confirmed that two novel bio-based polyols, PSiTh and PSiAm, were obtained through the ring opening of epoxy by the mercapto and amino moieties of MPTMS and APTES, respectively. Polyurethanes of these polyols were prepared using 4,4'- methylene-bis(phenyl isocyanate) (MDI) to incorporate silanol groups into polymer network and were labeled as PUSiTh and PUSiAm, respectively. To see the impact of silanol and phosphorous groups on flame retardant properties, the chain extended polyurethanes, PUSiThCE and PUSiAmCE were also prepared with bisphenol-A bis (hydroxy phenyl phosphonate) (BABHPP). Polyurethanes bearing thio-ether bonds besides alkoxy silane groups were characterized using FTIR spectroscopy. Prepared foams exhibited significant thermal stability and flame retardant properties with a limiting oxygen index (LOI) of 22-24%. Chain extended polyurethanes had 11-13% higher LOI value than the corresponding non-chain extended polyurethanes.