Abstract The design of ductile heterogeneous metallic glasses (MGs) with enhanced deformability by purposely controlling the shear-band dynamics via modulation of the atomic-scale structures and local stress states remains a significant challenge. Here, we correlate the changes in the local atomic structure when cooling to cryogenic temperature with the observed improved shear stability. The enhanced atomic-level structural and elastic heterogeneities related to the nonaffine thermal contraction of the short-range order (SRO) and medium-range order (MRO) change the characteristics of the activation process of the shear transformation zones (STZs). The experimental observations corroborated by Eshelby inclusion analysis and molecular dynamics simulations disclose the correlation between the structural fluctuations and the change in the stress field around the STZ. The variations in the inclination axes of the STZs alter their percolation mechanism, affect the shear-band dynamics and kinetics, and consequently delay shear failure. These results expand the understanding of the correlation between the atomic-level structure and elementary plastic events in monolithic MGs and thereby pave the way for the design of new ductile metallic alloys.