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In this study, we investigate the changes in the crystalline structure of MBE-deposited SrTiO3 layers on Si with different deviations from Sr/Ti stoichiometry as deposited but also after annealing at high temperatures (>600 °C). We show that as-grown 15 nm thick non-stochiometric SrTiO3 layers present surprisingly lower FWHM values of the (002) omega diffraction peak compared to fully stoichiometric layers of similar thickness. This can misleadingly point to superior crystalline quality of such non-stochiometric layers. However, thermal post-deposition anneals of these layers at temperatures up to 850 °C in oxygen show strong detrimental effects on the crystalline structure, surface and interface with the Si (001) substrate. On the contrary, the post-deposition anneals applied to the stoichiometric samples strongly improve the physical, optical and electrical properties of the epitaxial SrTiO3 thin films.