Inorganic or organic nanoparticles are often incorporated into foods to enhance their quality, stability, nutrition, or safety. When they pass through the gastrointestinal environment, the properties of these nanoparticles are altered, which impacts their biological effects and potential toxicity. Consequently, there is a need to understand how different kinds of nanoparticles behave within the gastrointestinal tract. In this article, the current understanding of the gastrointestinal fate of nanoparticles in foods is reviewed. Initially, the fundamental physicochemical and structural properties of nanoparticles are discussed, including their compositions, sizes, shapes, and surface chemistries. Then, the impact of food matrix effects and gastrointestinal environments on the fate of ingested nanoparticles is discussed. In particular, the influence of nanoparticle properties on food digestion and nutraceutical bioavailability is highlighted. Finally, future research directions are highlighted that will enable the successful utilization of nanotechnology in foods while also ensuring they are safe.