Electron microscopy has been applied widely to study the interaction of nanomaterials with proteins, cells and tissues at nanometre scale. Biological material is most commonly embedded in thermoset resins to make it compatible with the high vacuum in the electron microscope. Room temperature sample preparation protocols developed over decades provide contrast by staining cell organelles, and aim to preserve the native cell structure. However, the effect of these complex protocols on the nanomaterials in the system is seldom considered. Any artefacts generated during sample preparation may ultimately interfere with the accurate prediction of the stability and reactivity of the nanomaterials. As a case study, we review steps in the room temperature preparation of cells exposed to silver nanomaterials (AgNMs) for transmission electron microscopy imaging and analysis. In particular, embedding and staining protocols, which can alter the physicochemical properties of AgNMs and introduce artefacts thereby leading to a misinterpretation of silver bioreactivity, are scrutinized. Recommendations are given for the application of cryogenic sample preparation protocols, which simultaneously fix both particles and diffusible ions. By being aware of the advantages and limitations of different sample preparation methods, compromises or selection of different correlative techniques can be made to draw more accurate conclusions about the data. Lay description: With increasing commercialization of silver nanomaterials (AgNMs) comes a concomitant need to understand occupational health, public safety and environmental implications of these materials. Nanoscale studies of the complex bio-nano interface lie at the heart of technical challenges. Despite numerous reports, there is no consensus regarding biological mechanisms enacted by AgNMs. Powerful new electron microscopy techniques can be used to visualize the interaction of the AgNMs with tissues. However, it is extremely difficult to preserve this nanomaterial within cells or tissues for imaging in these microscopes, to be able to accurately see how it behaves. The reason for this is that AgNMs can dissolve or change its chemistry in air, or in artificial fluids and chemicals, which are used to fix the structure of tissues to be able to visualize the NMs in electron microscopes. Unless great care is taken when preparing these materials, artefacts produced will lead us to incorrect conclusions about how they react with tissues. For example, we could incorrectly conclude that they can dissolve and interact with the nucleus causing genetic damage, when in fact, in the body they dissolve and form a nontoxic material, which does not cause any toxicity to the cells. Preparing samples for high powered microscopy analysis is a multistep process and the AgNMs may be susceptible to dissolution during each step. There has been an explosion in the literature concerning the toxicity of engineered nanomaterials; however, few papers consider whether or not the nanomaterial changes its format in body or during processing, so it is difficult to draw conclusions. The aim of this review is to discuss the pitfalls that can be made during preparation of these materials for microscopy and provide recommendations about how to prepare AgNMs, without creating unwanted artefacts.