From the large number of methods used for the long-term preservation of microorganisms, the most effective are cryopreservation and lyophilization. Lyophilization is a method of preserving microorganisms, which consists of the freeze-drying process based on the removal of water from the frozen cellular material, by sublimation in a vacuum. Freezing plays an important role in the lyophilization process, as well as the lyoprotectors used. In this study, the lyoprotective medium used for lyophilization of micromycetes was supplemented with nanoparticles of Fe₂O₃, Fe₂ZnO₄, and ZnO. As a result of the evaluation of the viability of micromycetes of the genus Aspergillus, Trichoderma, and Penicillium after lyophilization and 1 year of storage in a lyophilized state, a stimulation of viability was obtained in the variants with Fe₂O₃ and Fe₂ZnO₄ nanoparticles in a concentration of 5.0 mg/L, and in the variants with ZnO nanoparticles after lyophilization.