Engineered nanomaterials (ENMs) are increasingly being used in the food industry. In order to assess the efficacy and the risks of these materials, it is essential to have access to methods that not only detect the nanomaterials, but also provide information on the characteristics of the materials (e.g., size and shape). This review presents an overview of electron microscopy (EM)-based methods that have been, or have the potential to be, applied to imaging ENMs in foodstuffs. We provide an overview of approaches to sample preparation, including drying, chemical treatment, fixation and cryogenic methods. We then describe standard and non-standard EM-based approaches that are available for imaging prepared samples. Finally, we present a strategy for selecting the most appropriate method for a particular foodstuff.