The large plasticity observed in newly developed monolithic bulk metallic glasses under quasi-static compression raises a question about the contribution of atomic scale effects. Here, nanocrystals on the order of 1-1.5 nm in size are observed within an Fe-based bulk metallic glass using aberration-corrected high-resolution transmission electron microscopy (HRTEM). The accumulation of nanocrystals is linked to the presence of hard and soft zones, which is connected to the micro-scale hardness and elastic modulus confirmed by nanoindentation. Furthermore, we performed systematic simulations of HRTEM images at varying sample thicknesses, and established a theoretical model for the estimation of the shear transformation zone size. The findings suggest that the main mechanism behind the formation of softer regions are the homogenously dispersed nanocrystals, which are responsible for the start and stop mechanism of shear transformation zones and hence, play a key role in the enhancement of mechanical properties.