The rapid development of nanotechnology provides new approaches to manufacturing food-related nanoparticles in various food industries, including food formulation, functional foods, food packaging, and food quality control. Once ingested, nanoparticles will immediately adsorb proteins in the biological fluids, forming a corona around them. Protein coronas alter the properties of nanoparticles, including their toxicity, cellular uptake, and targeting characteristics, by altering the aggregation state. In addition, the conformation and function of proteins and enzymes are also influenced by the formation of protein coronas, affecting the digestion of food products. Since the inevitable application of nanoparticles in food industries and their subsequent digestion, a comprehensive understanding of protein coronas is essential. This systematic review introduces nanoparticles in food and explains the formation of protein coronas, with interactions between proteins and nanoparticles. Furthermore, the potential origin of nanoparticles in food that migrate from packaging materials and their fates in the gastrointestinal tract has been reviewed. Finally, this review explores the possible effects of protein coronas on bioactive compounds, including probiotics and prebiotics. Understanding the formation mechanisms of protein coronas is crucial, as it enables the design of tailored delivery systems to optimize the bioavailability of bioactive compounds.