Activity study of the titanosilicate zeolites in liquid-phase oxidation reactions has received significant attention up to this point, whereas less effort has been made on structural stability. Here, we report catalytic activity and structural stability assessment of a supported embryonic TS-1 (E-TS-1) and 2 μm (μm)-sized crystalline TS-1 zeolites synthesized under different strategies in the oxidative desulfurization reaction (ODS) in the presence of varying amounts of water. The desulfurization activity of the TS-1 catalysts decreased significantly with the amount of water in the ODS reaction, while the silanized TS-1 catalysts showed higher activity than the pristine TS-1 catalysts and slowed Ti leaching. FTIR, SAED, TEM-EDX, SEM-EDX, HRTEM, FE-SEM, N₂ sorption, and drift UV–Vis were among the analytical techniques utilized to thoroughly investigate the structural stability of the (silanized) TS-1 and those recovered from the ODS processes from the nano-to macro-scale. For the first time, we describe how the ODS reactions causes detachment of the μm-sized (silanized) TS-1 crystals into primary amorphous nanoparticles through the adverse of non-classical crystallization as the primary mechanism. The degree to which the (silanized) TS-1 crystals detach and undergo morphological changes was influenced by the synthesis strategy, catalytic turnover, and reaction conditions. Large crystals dissolution into amorphous nanoparticles and Ti leaching account for the loss of solids and decline in activity of TS-1 zeolites in liquid-phase oxidation processes. This would help in the development of more robust catalysts to support their practical uses.