The effect of heat treatment on the structure and mechanical properties of Co-Fe-Cr-Si-B/Fe-Cr-B/Fe-Ni-B amorphous alloys has been studied systematically. Melt-quenching (spinning method) was used for production of investigated amorphous alloys. The transmission electron microscopy (TEM) was used to study the structure transformations. The effect of temperature on deformation behavior (plasticity, microhardness, crack resistance, and the density and average length of shear bands) of the amorphous alloys was studied by bending and microindentation. It is shown that the ductile–brittle transition, which occurs at the stage of structure relaxation in amorphous alloys, is caused by two factors: a decrease in the susceptibility of the amorphous matrix to plastic flow and an abrupt decrease in the resistance to the development of quasibrittle cracks. It is established that the transition to a two-phase amorphous–nanocrystalline state upon annealing leads to substantial strengthening of the alloys and a partial recovery of their plasticity. It is proved that the strengthening of amorphous alloys at the initial stages of crystallization can be initiated by the difference in the elastic moduli of the amorphous matrix and the precipitated nanocrystals, as well as by the specific features of the interaction between nanocrystalline phase particles and shear bands propagating under external actions. It is established that the phenomenon of plasticization in amorphous alloys (the crack resistance can increase after annealing in a certain temperature range) is due to the effective retardation of cracks on nanoparticles.