Electron microscopy (EM) has emerged as a vital technique for the detection and characterization of plant viruses. Its unparalleled resolution allows for the direct visualization of viral particles, facilitating the identification of viruses that are otherwise difficult to detect with traditional methods. Electron microscopy, considered by some to be an old technique, is still on the forefront of both clinical viral diagnoses and viral ultrastructure and pathogenesis studies. Using the most up-to-date electron cryomicroscopy methods and ongoing technical improvements offers a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. This study reviews the application of electron microscopy in plant virology, highlighting the different methodologies and materials used. We discuss the preparation techniques, including negative staining, thin sectioning, immunoelectron microscopy, and combinated use of TEM and SEM that enhance viral particle visibility and identification.