Food ingredients present in the form of engineered nanoparticles (NPs) require specific labeling as “nano” in the European Union. Enforcing proper labeling of “nano” labeling poses several analytical challenges. This includes the many potential sources of NPs in food which can interfere with the analysis, the challenges in relation to sample preparation, the limitations of existing analytical techniques, and the lack of validated studies and reference materials. This book chapter summarizes these challenges and, in addition, suggests a screening strategy for inorganic NPs in food. It further highlights the future challenges of analyzing organic and carbon-based nanomaterials.