Nanotechnology offers a wide range of applications in the food sector such as development of new tastes and textures, nanoencapsulation of bioactive food components, design of nutrient delivery systems, nanosensors to detect spoilage or contamination, and the design of new food packaging materials. Although metal-based nanoparticles (AgNPs, SiO2NPs, TiO2NPs, ZnONPs...) have extensively been applied due to their antimicrobial, antioxidant and UV-blocking properties, there is limited knowledge about the impact of nanoparticles on human health and environment. For safety reasons, the EU has issued regulations requiring labelling of the nanomaterials in the ingredients list. Therefore, new analytical methods should be used to characterize nanomaterials but, since there is no single and universal method that can be applied to fully characterize nanoparticles, the need for multimethod approaches is widely acknowledged. This chapter focuses primarily on the application of metal-based nanoparticles in the food sector and the analytical methodologies used for nanoparticle characterization. Regarding the applications of nanoparticles, special attention should be paid to their antimicrobial properties and their use for developing active food packaging materials. Since the characterization of nanoparticles in complex matrices is troublesome, a detailed description of the prospects and difficulties of the analytical techniques commonly employed is given. Similarly, factors affecting nanoparticles stability such as sample preparation, interaction with food matrices, food stimulants, and chemicals used in “in vitro” gastric digestion procedures are also described. Finally, EU regulatory guidelines on nanomaterials are included and discussed.