Engineered nanomaterials undergo a dynamic interaction with matrices such as soil, water, and biological tissues in their lifetime. The investigation and assessment of these interactions is the key to understand the implications that nanotechnology has on different aspects, including biotoxicity, therapeutic efficacy, and overall environmental sustainability. Electron microscopy (EM) is a high-resolution imaging technique that has been rapidly developed to achieve in situ, in vitro, and realtime imaging of nanomaterials in biological matrices. This perspective is the first to review the recent progress on assessing nanobio interaction at different biological levels using EM. We provide a clear picture of different EM configurations with their overall properties and a systematic summary of three main sample preparation methods, such as nanomaterials in dehydrated, frozen, and hydrated matrices. This perspective also provides a thorough discussion on the findings of the past five years on nanobio assessments using EM, such as the identification of nanocorona formation inside seeds during nanoagricultural studies; near-native structural analysis of lipid nanoparticles in nanomedicine studies; and the real-time observation of tumor cell internalization of gold nanoparticle in cancer research. Solving how engineered nanomaterials behave in a biological matrix has made a qualitative leap in nanoresearch. By summarizing recent studies, this perspective discusses the benefits and overall pitfalls of EM in aspects such as the resolution, sampling, and cost.