For bulk metallic glasses (BMGs) structural anisotropy has been studied for many years, but usually for small creep strains, rather than for large strains associated with the viscoplastic flow. In this study, the structural modifications in the short-to-medium range order of Zr55Cu30Al10Ni5 BMG is deliberated for the first time upon simultaneous high-pressure torsion (HPT) and in-situ annealing around the glass transition temperature (Tg). The changes are evaluated in terms of hardness by microindentation, thermal properties by differential thermal calorimetry, chemistry by energy dispersive X-ray, and structural properties by synchrotron X-ray diffraction and transmission electron microscopy. A remarkable increase of the glass transition temperature and the absence of the shoulder of the crystallization peak along with remarkable softening and shear thinning reveals that even at Tg the material gains flow characteristics because of the extreme pressure applied. A clear shift towards smaller wave vector Q in the peak positions of the partial distribution function G(r), and reconfiguration of the bonding between Zr−Zr and Zr−Cu atomic pairs extracted from the deconvolution of the radial distribution function RDF(r) are observed with changing the processing temperature. The findings give insight into the atomic and nano-scale modifications in BMGs due to high-pressure torsion at different temperatures which would be essential to tune the intrinsic properties of BMGs to attain the desirable hardness and thermal stability for a specific application.