By performing extensive molecular dynamics simulations, we investigate the deformation behavior in Al90Sm10 and Cu64.5Zr35.5 alloys after elongated isothermal annealing in the vicinity of the glass-transition temperature (Tg). Different microstructural response to the annealing process was observed: Al90Sm10 maintains the glassy structure with improved energetic stability, enhanced short-range order (SRO), and a more pronounced spatial network that extends beyond the first atomic shell, while Cu64.5Zr35.5 forms nanocrystalline Laves Cu2Zr phases. Shear banding occurs in both annealed systems under shear loading. For Al90Sm10, the spatial network formed by the local clusters characterizing the SRO of the system is significantly weakened but remains appreciable in the shear band. In contrast, the crystalline ordering in the Cu64.5Zr35.5 is completely destroyed during shear banding. Consequently, while displaying higher yield strength, the annealed Cu64.5Zr35.5 sample appears to be less ductile. By carefully examining the effect of microstructures on the structural ordering in the shear band and the consequent mechanical response, our work contributes to a better understanding of the deformation mechanism of amorphous alloys as compared with that in crystalline materials.