Recent advancements in amorphous materials have opened new avenues for exploring unusual magnetic phenomena at the sub-nanometer scale. We investigate the phenomenon of low-temperature “magnetic hardening” in heterogeneous amorphous Fe–Ni–B–Nb thin films, revealing a complex interplay between microstructure and magnetism. Magnetization hysteresis measurements at cryogenic temperatures show a significant increase in coercivity (HC) below 25 K, challenging the conventional Random Anisotropy Model (RAM) in predicting magnetic responses at cryogenic temperatures. Heterogeneous films demonstrate a distinct behavior in field-cooled and zero-field-cooled temperature-dependent magnetizations at low temperatures, characterized by strong irreversibility. This suggests spin-glass-like features at low temperatures, which are attributed to exchange frustration in disordered interfacial regions. These regions hinder direct exchange coupling between magnetic entities, leading to magnetic hardening. This study enhances the understanding of how microstructural intricacies impact magnetic dynamics in heterogeneous amorphous thin films at cryogenic temperatures.