Cryo-electron microscopy (cryo-EM) is indispensable for the structural studies of enveloped viruses: dangerous pathogens of humans and animals. Yet, it requires highly specialized equipment as well as careful sample preparation. In this work, the capabilities of a JEOL JEM-2100 transmission electron microscope equipped with a cryo-transfer holder are used, and preliminary cryo-EM data for influenza A and B virus strains and SARS-CoV-2 inactivated with beta-propiolactone are presented. Image analysis allows us to (1) distinguish “empty” viral particles from “full” ones (containing nucleocapsid); (2) visualize the lipid bilayer of the viral envelope; (3) identify influenza virus surface antigens and the M1 protein layer combined with the inner lipid monolayer; and (4) distinguish different morphology of S-spikes on the surface of inactivated SARS-CoV-2 virions. The developed approach provides good image quality for both fundamental and applied research.